date:20100102

I would like a scatterplot matrix and a correlation matrix for the
following set-up.
The data (dataframe d) are like this:

angle  resp
-90  182
-60  137
-30  ...etc
0
30
60
90
...etc

I would like each cell in the matrix to be the scatterplot of the
responses for each pair of angles ( -90 vs -60, -90 vs -30, etc). Same
for the correlation matrix.

Please tell me what to do. Thanks very much!

Bill

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[R] Regexp: extract first occurrence of date in string

I would like to extract first date from a string:

 txt - first date is 05.12.2009. Second date is 06.12.2009.
 txt
[1] first date is 05.12.2009. Second date is 06.12.2009.

I tried:

 sub(^.*?\\s(\\d{1,2}\\.\\d{1,2}\\.\\d{4}), \\1, txt, extended=T, perl=T)
[1] 05.12.2009. Second date is 06.12.2009.


How to modify this?

-J

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Re: [R] Question on Reduce + rollmean

Try apply:

library(zoo) # rollmean

# test data
m - matrix(1:3, 3, 3)
x - list(m, m+3, m+6)

# convert to array
a - array(unlist(x), c(3, 3, 3)); a

# apply rollmean and permute to desired form
aa - apply(a, 1:2, rollmean, k = 2)
aperm(aa, c(2, 3, 1))

The last line outputs:

 aperm(aa, c(2, 3, 1))
, , 1

 [,1] [,2] [,3]
[1,]  2.5  2.5  2.5
[2,]  3.5  3.5  3.5
[3,]  4.5  4.5  4.5

, , 2

 [,1] [,2] [,3]
[1,]  5.5  5.5  5.5
[2,]  6.5  6.5  6.5
[3,]  7.5  7.5  7.5


On Sat, Jan 2, 2010 at 10:00 AM, Muhammad Rahiz
muhammad.ra...@ouce.ox.ac.uk wrote:
 Let me rephrase;

 Given x as

 x

 [[1]]
  V1 V2 V3
 [1,]  1  1  1
 [2,]  2  2  2
 [3,]  3  3  3

 [[2]]
  V1 V2 V3
 [1,]  4  4  4
 [2,]  5  5  5
 [3,]  6  6  6

 [[3]]
  V1 V2 V3
 [1,]  7  7  7
 [2,]  8  8  8
 [3,]  9  9  9

 I'd like to calculate the moving average (interval = 2) i.e.

 ( x[[1]] + x[[2]] ) / 2
 ( x[[2]] + x[[3]] ) / 2
 ... and so on.

 The desired output will return

 2.5 2.5 2.5
 3.5 3.5 3.5
 4.5 4.5 4.5

 5.5 5.5 5.5
 6.5 6.5 6.5
 7.5 7.5 7.5




 Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling
 Climate Research Laboratory, School of Geography  the Environment
 Oxford University Centre for the Environment, University of Oxford
 South Parks Road, Oxford, OX1 3QY, United Kingdom
 Tel: +44 (0)1865-285194  Mobile: +44 (0)7854-625974
 Email: muhammad.ra...@ouce.ox.ac.uk



 milton ruser wrote:

 Dear M.Rahiz,

 Unfortunatelly I can't reproduce your example.
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html

 bests

 milton
 On Sat, Jan 2, 2010 at 9:26 AM, Muhammad Rahiz
 muhammad.ra...@ouce.ox.ac.ukmailto:muhammad.ra...@ouce.ox.ac.uk wrote:
 Hello useRs,

 I'd like to perform a moving average on the dataset, xx. I've tried
 combining the functions Reduce and rollmean but it didn't work.



 r - function(n) rollmean(n, 2) # where 2 = averaging interval
 output  - Reduce(r, x)


 Error in f(init, x[[i]]) : unused argument(s) (x[[i]])

 Is there anything wrong with the code in the first place?

 where


 x


 [[1]]
   V1 V2 V3
 [1,]  1  1  1
 [2,]  2  2  2
 [3,]  3  3  3

 [[2]]
   V1 V2 V3
 [1,]  4  4  4
 [2,]  5  5  5
 [3,]  6  6  6

 [[3]]
   V1 V2 V3
 [1,]  7  7  7
 [2,]  8  8  8
 [3,]  9  9  9

 The moving average is to be performed on

 1,4,7 = (1+4)/2 , (4+7)/2
 2,5,8 = ..
 3,6,9 = ..

 Thanks

 Muhammad

 --
 Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling
 Climate Research Laboratory, School of Geography  the Environment
 Oxford University Centre for the Environment, University of Oxford
 South Parks Road, Oxford, OX1 3QY, United Kingdom
 Tel: +44 (0)1865-285194  Mobile: +44 (0)7854-625974
 Email: muhammad.ra...@ouce.ox.ac.ukmailto:muhammad.ra...@ouce.ox.ac.uk

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Re: [R] Regexp: extract first occurrence of date in string

Try this which uses a slightly simpler regexp:

 library(gsubfn)
 strapply(txt, (\\d{1,2}\\.\\d{1,2}\\.\\d{4}).*)[[1]]
[1] 05.12.2009

or we could convert it to Date class at the same time where we have
assumed month.day.year:

 strapply(txt, (\\d{1,2}\\.\\d{1,2}\\.\\d{4}).*, ~ as.Date(x, 
 %m.%d.%Y))[[1]]
[1] 2009-05-12

or this even simpler regexp extracting all the dates and then picking
off the first:

 strapply(txt, \\d{1,2}\\.\\d{1,2}\\.\\d{4})[[1]][1]
[1] 05.12.2009

On Sat, Jan 2, 2010 at 10:08 AM, johannes rara johannesr...@gmail.com wrote:
 I would like to extract first date from a string:

 txt - first date is 05.12.2009. Second date is 06.12.2009.
 txt
 [1] first date is 05.12.2009. Second date is 06.12.2009.

 I tried:

 sub(^.*?\\s(\\d{1,2}\\.\\d{1,2}\\.\\d{4}), \\1, txt, extended=T, perl=T)
 [1] 05.12.2009. Second date is 06.12.2009.


 How to modify this?

 -J

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


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Re: [R] Regexp: extract first occurrence of date in string

Thanks, is the same possible using basic gsub/sub/grep etc. functions?

-J

2010/1/2 Gabor Grothendieck ggrothendi...@gmail.com:
 Try this which uses a slightly simpler regexp:

 library(gsubfn)
 strapply(txt, (\\d{1,2}\\.\\d{1,2}\\.\\d{4}).*)[[1]]
 [1] 05.12.2009

 or we could convert it to Date class at the same time where we have
 assumed month.day.year:

 strapply(txt, (\\d{1,2}\\.\\d{1,2}\\.\\d{4}).*, ~ as.Date(x, 
 %m.%d.%Y))[[1]]
 [1] 2009-05-12

 or this even simpler regexp extracting all the dates and then picking
 off the first:

 strapply(txt, \\d{1,2}\\.\\d{1,2}\\.\\d{4})[[1]][1]
 [1] 05.12.2009

 On Sat, Jan 2, 2010 at 10:08 AM, johannes rara johannesr...@gmail.com wrote:
 I would like to extract first date from a string:

 txt - first date is 05.12.2009. Second date is 06.12.2009.
 txt
 [1] first date is 05.12.2009. Second date is 06.12.2009.

 I tried:

 sub(^.*?\\s(\\d{1,2}\\.\\d{1,2}\\.\\d{4}), \\1, txt, extended=T, perl=T)
 [1] 05.12.2009. Second date is 06.12.2009.


 How to modify this?

 -J

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



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Re: [R] Regexp: extract first occurrence of date in string

Use regexpr to get the offset into the string and its length and then
use substr to pick extract it.

On Sat, Jan 2, 2010 at 10:43 AM, johannes rara johannesr...@gmail.com wrote:
 Thanks, is the same possible using basic gsub/sub/grep etc. functions?

 -J

 2010/1/2 Gabor Grothendieck ggrothendi...@gmail.com:
 Try this which uses a slightly simpler regexp:

 library(gsubfn)
 strapply(txt, (\\d{1,2}\\.\\d{1,2}\\.\\d{4}).*)[[1]]
 [1] 05.12.2009

 or we could convert it to Date class at the same time where we have
 assumed month.day.year:

 strapply(txt, (\\d{1,2}\\.\\d{1,2}\\.\\d{4}).*, ~ as.Date(x, 
 %m.%d.%Y))[[1]]
 [1] 2009-05-12

 or this even simpler regexp extracting all the dates and then picking
 off the first:

 strapply(txt, \\d{1,2}\\.\\d{1,2}\\.\\d{4})[[1]][1]
 [1] 05.12.2009

 On Sat, Jan 2, 2010 at 10:08 AM, johannes rara johannesr...@gmail.com 
 wrote:
 I would like to extract first date from a string:

 txt - first date is 05.12.2009. Second date is 06.12.2009.
 txt
 [1] first date is 05.12.2009. Second date is 06.12.2009.

 I tried:

 sub(^.*?\\s(\\d{1,2}\\.\\d{1,2}\\.\\d{4}), \\1, txt, extended=T, 
 perl=T)
 [1] 05.12.2009. Second date is 06.12.2009.


 How to modify this?

 -J

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




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Re: [R] Regexp: extract first occurrence of date in string

Thanks for the hint, ie. something like this works in this case:

 txt - first date is 05.12.2009. Second date is 06.12.2009.
 txt
[1] first date is 05.12.2009. Second date is 06.12.2009.
 l - regexpr(\\d{1,2}\\.\\d{1,2}\\.\\d{4}, txt, perl=T)
 substr(txt, l, l+9)
[1] 05.12.2009


But your examples are more generic. I'll have to look gsubfn more closely.

-J

2010/1/2 Gabor Grothendieck ggrothendi...@gmail.com:
 Use regexpr to get the offset into the string and its length and then
 use substr to pick extract it.

 On Sat, Jan 2, 2010 at 10:43 AM, johannes rara johannesr...@gmail.com wrote:
 Thanks, is the same possible using basic gsub/sub/grep etc. functions?

 -J

 2010/1/2 Gabor Grothendieck ggrothendi...@gmail.com:
 Try this which uses a slightly simpler regexp:

 library(gsubfn)
 strapply(txt, (\\d{1,2}\\.\\d{1,2}\\.\\d{4}).*)[[1]]
 [1] 05.12.2009

 or we could convert it to Date class at the same time where we have
 assumed month.day.year:

 strapply(txt, (\\d{1,2}\\.\\d{1,2}\\.\\d{4}).*, ~ as.Date(x, 
 %m.%d.%Y))[[1]]
 [1] 2009-05-12

 or this even simpler regexp extracting all the dates and then picking
 off the first:

 strapply(txt, \\d{1,2}\\.\\d{1,2}\\.\\d{4})[[1]][1]
 [1] 05.12.2009

 On Sat, Jan 2, 2010 at 10:08 AM, johannes rara johannesr...@gmail.com 
 wrote:
 I would like to extract first date from a string:

 txt - first date is 05.12.2009. Second date is 06.12.2009.
 txt
 [1] first date is 05.12.2009. Second date is 06.12.2009.

 I tried:

 sub(^.*?\\s(\\d{1,2}\\.\\d{1,2}\\.\\d{4}), \\1, txt, extended=T, 
 perl=T)
 [1] 05.12.2009. Second date is 06.12.2009.


 How to modify this?

 -J

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 http://www.R-project.org/posting-guide.html
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Re: [R] caculate the frequencies of the Amino Acids

2010-01-02 Thread Jorge Ivan Velez

Hi fadialnaji,

Take a look at the Biostring package in Bioconductor [1] It might be an
alternative to do what you want.

HTH,
Jorge

[1] http://www.bioconductor.org/packages/release/bioc/html/Biostrings.html


On Fri, Jan 1, 2010 at 11:59 PM, che  wrote:


 may some one please help me to sort this out, i am trying to writ a R code
 for calculating the frequencies of the amino acids in 9 different
 sequences,
 i want the code to read the sequence from external text file, i used the
 following code to do so:
 x-read.table(sequence.txt,header=FALSE)

 then i defined an array for 20 amino acids as following:

 AA-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
 i am using the following code to calculate the frequencies:

 frequency-function(X)
 {
 y-rep(0,20)
 for(j in 1:nchar(as.character(x$V1[i]))){
 for(i in 1:9){

res-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
}
}
 return(y)
 }

 but this code actually is not working, it reads only one sequence, i dont
 know why the loop is not working for the i, which suppose to read the
 nine
 rows of the file sequence.txt. the sequence.txt file is attached to this
 message.

 cheers
 http://n4.nabble.com/file/n997072/sequence.txt sequence.txt
 --
 View this message in context:
 http://n4.nabble.com/caculate-the-frequencies-of-the-Amino-Acids-tp997072p997072.html
 Sent from the R help mailing list archive at Nabble.com.

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[[alternative HTML version deleted]]

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Re: [R] Building static HTML help pages in R 2.10.x on Windows

2010-01-02 Thread Uwe Ligges




Steve Rowley wrote:

Heinz Tuechler wrote:

At 21:40 22.12.2009, Steve Rowley wrote:

(a) how to build the static HTML help pages of all currently
installed packages under Windows, [...]

At least two ways:

Way 1: reinstall all those packages from sources using
  R CMD INSTALL --html

Way 2: go to the man directory of a source package and apply
  R CMD Rdconv --type=html *.Rd
to all Rd files.


Ok, thanks.  That's starting along a helpful path.

The first way sounds dicey on Windows, since some of the packages require tools 
that I
probably have installed (e.g., as part of Cygwin), but have never thought about 
how to
hook together.

The second way sounds useful if I want to download the source for all the 
packages in
addition to the binary installers that I already have.

Is there any way to do this from the Windows binary .zip files, or from the 
installations
generated thereby?  After all, R generates the HTML on the fly somehow, so the 
information
is present; IWBNI there were a way to use that to generate the static HTML.  
(Looking
through the installation dirs doesn't show very many .Rd files.)



Ah, sorry, I must have missed your reply.

WEell, internally, you can do somewthing as R's help system does, but it 
is documented to be subject to change (As they are mainly intended for 
internal use, their interfaces are subject to change.), see ?Rd2HTML


For package pkg in directory c:/dir on help topic foo you could ask

Rd2HTML(tools:::fetchRdDB(c:/dir/pkg/help/pkg, foo)) in order to get 
a HTML representation. See ?Rd2HTML for details on how to control stuff.


Uwe Ligges

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Re: [R] How to calculate density function of Bivariate binomial distribution

2010-01-02 Thread nykee

Thanks milton,

I checked some of them, and actually none is what I want. So instead, I
wrote a small function for the density of bivariate binomial. Thanks,

nykee

milton ruser wrote:

Hi Nykee,

I checked out ??bivariate on my R installed libraries,
and found about a hundred of occurrences of bivariate.
If nobody reply you with a streigth answer, give a look at:
VGAM; splancs; sm; prada; geoR; fUtilities; fBasics;
akima; adehabitat; vegan; ade4 and spatstat packages.

bests

milton

On Fri, Jan 1, 2010 at 5:36 PM, nykee rairai...@hotmail.com wrote:

Am trying to do some study on bivariate binomial distribution. Anyone
knows
if there is package in R that I can use to calculate the density function
of
bivariate binomial distribution and to generate random samples of it.
Thanks,

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[[alternative HTML version deleted]]

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[R] Query: sampling from a multivariate normal distribution using the singular value decomposition

2010-01-02 Thread Stefano Sofia

Dear R-list users,
this question is not strictly related to R, but hopefully somebody will be able 
to answer.
In a schematic way, which is the algorithm to sample from a multivariate normal 
distribution using the singular value decomposition?

thank you for your help
Stefano

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Re: [R] scatterplot matrix question

2010-01-02 Thread Charles C. Berry


On Sat, 2 Jan 2010, William Simpson wrote:


I would like a scatterplot matrix and a correlation matrix for the
following set-up.
The data (dataframe d) are like this:

angle  resp
-90  182
-60  137
-30  ...etc
0
30
60
90
...etc

I would like each cell in the matrix to be the scatterplot of the
responses for each pair of angles ( -90 vs -60, -90 vs -30, etc). Same
for the correlation matrix.

Please tell me what to do. Thanks very much!


1) You need to provide commented, minimal, self-contained, reproducible
   code.

2) You need to fill in some missing info: Either you have only one
   response for each angle, or you need a third variable to pair up the
   corresponding responses for one angle with those of another.

Chuck



Bill

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NOTE:.^






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

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[R] filehash - multiple indices via '[' not allowed when using RDS format

2010-01-02 Thread Hao Cen

Hi,

I have been using filehash for a while. It has performed very well.
However, recently I found filehash gives an error when I need to do
something like db[c(a, b)] when the db is in RDS format. Does any one
know a way to get around that?

The code below reproduces the error

thanks

Jeff

filehashOption(defaultType = DB1)
dbCreate(mydb3, type = DB1)
db = dbInit(mydb3)
db$a = rnorm(100, 1)
db$b = rnorm(100, 1)
with(db, c(a = mean(a), b = mean(b)))
sapply(db[c(a, b)], mean)  # works.


filehashOption(defaultType = RDS)
dbCreate(mydb4, type = RDS)
db = dbInit(mydb4)
db$a = rnorm(100, 1)
db$b = rnorm(100, 1)
with(db, c(a = mean(a), b = mean(b)))
sapply(db[c(a, b)], mean)  # not work

Error in .local(x, i, j, ..., drop) :
  multiple indices via '[' not allowed
Calls: sapply - lapply - is.vector - [ - [ - .local
[1] 7: stop(\multiple indices via '[' not allowed\)
[1] 6: .local(x, i, j, ..., drop)
[1] 5: db[c(\a\, \b\)]
[1] 4: db[c(\a\, \b\)]
[1] 3: is.vector(X)
[1] 2: lapply(X, FUN, ...)
[1] 1: sapply(db[c(\a\, \b\)], mean)


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

Re: [R] scatterplot matrix question

On Sat, Jan 2, 2010 at 4:55 PM, Charles C. Berry cbe...@tajo.ucsd.edu wrote:
 On Sat, 2 Jan 2010, William Simpson wrote:

 I would like a scatterplot matrix and a correlation matrix for the
 following set-up.
 The data (dataframe d) are like this:

 angle  resp
 -90  182
 -60  137
 -30  ...etc
 0
 30
 60
 90
 ...etc

 I would like each cell in the matrix to be the scatterplot of the
 responses for each pair of angles ( -90 vs -60, -90 vs -30, etc). Same
 for the correlation matrix.

 Please tell me what to do. Thanks very much!

 1) You need to provide commented, minimal, self-contained, reproducible
   code.
d-read.table(rstuff/data.dat,header=TRUE)

Now what? :-)

certainly it's not
pairs(d)


 2) You need to fill in some missing info: Either you have only one
   response for each angle, or you need a third variable to pair up the
   corresponding responses for one angle with those of another.
contents of rstuff/data.dat:

 angle  resp  ID
 -90  182  1
 -60  137  1
 -30  123  1
 067  1
 30   32  1
 60   12  1
 9013  1
-90  178  2
 -60  111  2
 -30  137  2
 094  2
 30   59  2
 60   1  2
 9019  2

I actually have a lot more than 2 experimental units (ID)...

Thanks for any help
Bill

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Re: [R] help with for loop

2010-01-02 Thread Bert Gunter

If I understand the query,

z - outer(x,x,-)
z[lower.tri(z)]  ## is what you want.

?outer and ?lower.tri  will tell you how to interpret what you get.

Bert Gunter
Genentech Nonclinical Statistics


-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of jim holtman
Sent: Friday, January 01, 2010 5:25 PM
To: Rafael Moral
Cc: r-help
Subject: Re: [R] help with for loop

Look at your function; it is returning exactly what you are asking for:

x.dif - c(diff(my.vec), diff(my.vec, lag=i))  # the first and last values

You probably want something like this:

dif - function(my.vec) {
x.diff - diff(my.vec)
for(i in 2:(length(my.vec)-1)) {
x.dif - c(x.diff, diff(my.vec, lag=i))
}
return(x.dif)
}

You might also want to check if the length of the vector is 2, or less,
since your 'for' will not work.
On Fri, Jan 1, 2010 at 8:16 PM, Rafael Moral
rafa_moral2...@yahoo.com.brwrote:

 Dear useRs,

 I want to write a function that generates all the possible combinations of
 diff().

 Example:
 If my vector has length 5, I need the diff() until lag=4 -
 c(diff(my.vec), diff(my.vec, lag=2), diff(my.vec, lag=3), diff(my.vec,
 lag=4))

 If it has length 4, I need until lag=3 -
 c(diff(my.vec), diff(my.vec, lag=2), diff(my.vec, lag=3))

 So, it must be until lag=(length(my.vec)-1).

 The function I've written is:
 dif - function(my.vec) {
 for(i in 2:(length(my.vec)-1)) {
 x.dif - c(diff(my.vec), diff(my.vec, lag=i))
 }
 return(x.dif)
 }

 But it only returns the first diff() (lag=1) and the last one (
 diff(my.vec, lag=(length(my.vec)-1)   )
 Example:
  my.vec = c(1,2,3,2)
  dif(my.vec)
 [1]  1  1 -1  1
 What I wanted to get was:
  c(diff(my.vec), diff(my.vec, lag=2), diff(my.vec, lag=3))
 [1]  1  1 -1  2  0  1

 Is there a way of computing it so R understands what I want?

 Thanks in advance, happy new year for everyone!

 Kind regards,
 Rafael.






 [[elided Yahoo spam]]

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

Re: [R] scatterplot matrix question

2010-01-02 Thread Uwe Ligges




William Simpson wrote:

On Sat, Jan 2, 2010 at 4:55 PM, Charles C. Berry cbe...@tajo.ucsd.edu wrote:

On Sat, 2 Jan 2010, William Simpson wrote:


I would like a scatterplot matrix and a correlation matrix for the
following set-up.
The data (dataframe d) are like this:

angle  resp
-90  182
-60  137
-30  ...etc
0
30
60
90
...etc

I would like each cell in the matrix to be the scatterplot of the
responses for each pair of angles ( -90 vs -60, -90 vs -30, etc). Same
for the correlation matrix.

Please tell me what to do. Thanks very much!

1) You need to provide commented, minimal, self-contained, reproducible
  code.

d-read.table(rstuff/data.dat,header=TRUE)

Now what? :-)

certainly it's not
pairs(d)




Now that we are able to help with some more detailed view of your data 
(although you could have helped helping by making it easier for us to 
import your data into R), the answer is:


Almost, after reshaping:



dwide - reshape(d, v.names=resp, idvar=ID,
 timevar=angle, direction=wide)
pairs(dwide[,-1])


Best,
Uwe Ligges







2) You need to fill in some missing info: Either you have only one
  response for each angle, or you need a third variable to pair up the
  corresponding responses for one angle with those of another.

contents of rstuff/data.dat:

 angle  resp  ID
 -90  182  1
 -60  137  1
 -30  123  1
 067  1
 30   32  1
 60   12  1
 9013  1
-90  178  2
 -60  111  2
 -30  137  2
 094  2
 30   59  2
 60   1  2
 9019  2

I actually have a lot more than 2 experimental units (ID)...

Thanks for any help
Bill

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


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Re: [R] suppress output for meta in package tm

2010-01-02 Thread Amber Jaycocks

Hi, Peter.

Thanks.  This works but is not ideal to have an external file.  The main
reason I want to suppress the output is to speed up the processing time,
which capture.output does indeed do.  It is a great work around for now.

I am using the output to match items in a corpa to a file that contains
metadata and then attaching the fields in the meta data file as metadata to
each item in the corpa.  If you have any other suggestions to increase
processing speed please let me know.  Many Thanks.

for (n in 1:length(corpa)) {
n_corp_file - capture.output(meta(corpa[[n]], URI),file=log.txt)
#want just file not dir and file
n_char - nchar(n_corp_file[2])
#nchar[1] is file=4 and nchar[2] is dir + filename amd nchar[3] is UTF-8
= 5
n_char_dir - nchar(corpa_dir)
corp_file - substr(n_corp_file, n_char_dir + 2, n_char)
corp_file - corp_file[2]
#match corpa file with meta data file
match_index - match(corp_file,(meta_data$file))
if (!is.na(match_index)) {
#attach all rows of meta_data
meta_cols - colnames(meta_data)
for (col in 1:length(meta_cols)) {
meta(corpa[[n]], meta_cols[col]) - meta_data[match_index,meta_cols[col]] }
} #if
} #for n corpa

On Sat, Jan 2, 2010 at 6:03 AM, Peter Ehlers ehl...@ucalgary.ca wrote:

 Can you wrap your call in capture.output(..., file=...)?

  -Peter Ehlers

 Amber Jaycocks wrote:

  Hello,

 I am using the tm package and wish to suppress the output for meta.  I am
 defining another variable for one of the tags and don't want the value
 printed on the screen.  Any help would be appreciated.  Thanks.

 here is the commnad:

 n_corp_file - meta(corpa[[n]], URI)

 -Amber

[[alternative HTML version deleted]]

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



 --
 Peter Ehlers
 University of Calgary
 403.202.3921


[[alternative HTML version deleted]]

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

Re: [R] scatterplot matrix question

 Now that we are able to help with some more detailed view of your data
 (although you could have helped helping by making it easier for us to import
 your data into R), the answer is:
I am preparing for the data analysis, writing the code (knowing I may
have to modify it later) while the data are still being collected.
That's why I used the artificial data when asked for some. I will be
pressed for time when the data arrive.

 Almost, after reshaping:



 dwide - reshape(d, v.names=resp, idvar=ID,
 timevar=angle, direction=wide)
 pairs(dwide[,-1])


Thanks very much, Uwe. I will try this (on artificial data). I think
reshape() requires a library [reshape?].

Bill

__
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.

Re: [R] suppress output for meta in package tm

2010-01-02 Thread Peter Ehlers


I don't know anything about pkg:tm, but I'll make a
couple of comments below.

Amber Jaycocks wrote:

Hi, Peter.

Thanks.  This works but is not ideal to have an external file.  The main
reason I want to suppress the output is to speed up the processing time,
which capture.output does indeed do.  It is a great work around for now.

I am using the output to match items in a corpa to a file that contains
metadata and then attaching the fields in the meta data file as metadata to
each item in the corpa.  If you have any other suggestions to increase
processing speed please let me know.  Many Thanks.

for (n in 1:length(corpa)) {

or: for(n in seq_along(corpa)){


n_corp_file - capture.output(meta(corpa[[n]], URI),file=log.txt)

here, I think, you want:
capture.output(n_corp_file - meta(corpa[[n]], URI), file=log.txt)

and I would use (on Windows): file=clipboard


#want just file not dir and file
n_char - nchar(n_corp_file[2])
#nchar[1] is file=4 and nchar[2] is dir + filename amd nchar[3] is UTF-8
= 5
n_char_dir - nchar(corpa_dir)
corp_file - substr(n_corp_file, n_char_dir + 2, n_char)
corp_file - corp_file[2]
#match corpa file with meta data file
match_index - match(corp_file,(meta_data$file))
if (!is.na(match_index)) {
#attach all rows of meta_data
meta_cols - colnames(meta_data)
for (col in 1:length(meta_cols)) {
meta(corpa[[n]], meta_cols[col]) - meta_data[match_index,meta_cols[col]] }
} #if
} #for n corpa



You might also find sink() to be more to your taste than
capture.output().

 -Peter


On Sat, Jan 2, 2010 at 6:03 AM, Peter Ehlers ehl...@ucalgary.ca wrote:


Can you wrap your call in capture.output(..., file=...)?

 -Peter Ehlers

Amber Jaycocks wrote:


 Hello,

I am using the tm package and wish to suppress the output for meta.  I am
defining another variable for one of the tags and don't want the value
printed on the screen.  Any help would be appreciated.  Thanks.

here is the commnad:

n_corp_file - meta(corpa[[n]], URI)

-Amber

   [[alternative HTML version deleted]]

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




--
Peter Ehlers
University of Calgary
403.202.3921





--
Peter Ehlers
University of Calgary
403.202.3921

__
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.

Re: [R] scatterplot matrix question

2010-01-02 Thread David Winsemius



On Jan 2, 2010, at 1:49 PM, William Simpson wrote:

Now that we are able to help with some more detailed view of your  
data
(although you could have helped helping by making it easier for us  
to import

your data into R), the answer is:

I am preparing for the data analysis, writing the code (knowing I may
have to modify it later) while the data are still being collected.
That's why I used the artificial data when asked for some. I will be
pressed for time when the data arrive.


Almost, after reshaping:



dwide - reshape(d, v.names=resp, idvar=ID,
   timevar=angle, direction=wide)
pairs(dwide[,-1])



Thanks very much, Uwe. I will try this (on artificial data). I think
reshape() requires a library [reshape?].


No. In fact, the reshape package does not have a reshape function.

--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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

Re: [R] scatterplot matrix question

OK thanks David


 Thanks very much, Uwe. I will try this (on artificial data). I think
 reshape() requires a library [reshape?].

 No. In fact, the reshape package does not have a reshape function.

 --

 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT



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

Re: [R] suppress output for meta in package tm

2010-01-02 Thread jim holtman

Actually if you just use 'capture.output' without specifying a 'file' it
will return a character vector with the output which you can just ignore.

On Sat, Jan 2, 2010 at 1:51 PM, Peter Ehlers ehl...@ucalgary.ca wrote:

 I don't know anything about pkg:tm, but I'll make a
 couple of comments below.


 Amber Jaycocks wrote:

 Hi, Peter.

 Thanks.  This works but is not ideal to have an external file.  The main
 reason I want to suppress the output is to speed up the processing time,
 which capture.output does indeed do.  It is a great work around for now.

 I am using the output to match items in a corpa to a file that contains
 metadata and then attaching the fields in the meta data file as metadata
 to
 each item in the corpa.  If you have any other suggestions to increase
 processing speed please let me know.  Many Thanks.

 for (n in 1:length(corpa)) {

 or: for(n in seq_along(corpa)){


 n_corp_file - capture.output(meta(corpa[[n]], URI),file=log.txt)

 here, I think, you want:
 capture.output(n_corp_file - meta(corpa[[n]], URI), file=log.txt)

 and I would use (on Windows): file=clipboard


 #want just file not dir and file
 n_char - nchar(n_corp_file[2])
 #nchar[1] is file=4 and nchar[2] is dir + filename amd nchar[3] is
 UTF-8
 = 5
 n_char_dir - nchar(corpa_dir)
 corp_file - substr(n_corp_file, n_char_dir + 2, n_char)
 corp_file - corp_file[2]
 #match corpa file with meta data file
 match_index - match(corp_file,(meta_data$file))
 if (!is.na(match_index)) {
 #attach all rows of meta_data
 meta_cols - colnames(meta_data)
 for (col in 1:length(meta_cols)) {
 meta(corpa[[n]], meta_cols[col]) - meta_data[match_index,meta_cols[col]]
 }
 } #if
 } #for n corpa


 You might also find sink() to be more to your taste than
 capture.output().

  -Peter


 On Sat, Jan 2, 2010 at 6:03 AM, Peter Ehlers ehl...@ucalgary.ca wrote:

 Can you wrap your call in capture.output(..., file=...)?

  -Peter Ehlers

 Amber Jaycocks wrote:

  Hello,

 I am using the tm package and wish to suppress the output for meta.  I
 am
 defining another variable for one of the tags and don't want the value
 printed on the screen.  Any help would be appreciated.  Thanks.

 here is the commnad:

 n_corp_file - meta(corpa[[n]], URI)

 -Amber

   [[alternative HTML version deleted]]

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



 --
 Peter Ehlers
 University of Calgary
 403.202.3921



 --
 Peter Ehlers
 University of Calgary
 403.202.3921

  __
 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.htmlhttp://www.r-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.




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

What is the problem that you are trying to solve?

[[alternative HTML version deleted]]

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

Re: [R] Please help me!!!! Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected

2010-01-02 Thread Max Kuhn

Your data set has 217 predictors and 166 samples. If you read the
vignette on feature selection for this package, you'll see that the
default ranking mechanism that it uses for linear models requires a
linear model fit. The note that:

 prediction from a rank-deficient fit may be misleading

should tell you something. If it doesn't: the model fit is over
determined and there is no unique solution, so many of the parameter
estimates are NA.

Either create a modified version of lmFuncs that suits your needs or
remove variables prior to modeling (or try some other method that
doesn't require more samples than predictors, such as the lasso or
elasticnet).

Max

On Fri, Jan 1, 2010 at 10:14 PM, bbslover dlu...@yeah.net wrote:

 I am learning the package caret, after I do the rfe function, I get the
 error ,as follows:

 Error in `[.data.frame`(x, , retained, drop = FALSE) :
  undefined columns selected
 In addition: Warning message:
 In predict.lm(object, x) :
  prediction from a rank-deficient fit may be misleading


 I try to that manual example, that is good, my data is wrong. I do not know
 what reanson?

 my code is :

  subsets-c(1:5,10,15,20,25)
  ctrl-rfeControl(functions=lmFuncs, method  = cv,
            verbose=FALSE,returnResamp=final)
  lmProfile-rfe(trainDescr,trainY,sizes=subsets,rfeControl=ctrl)

 before it, I have do some pre-process and my data is in the attachment.

 Please help me.  thank you!

 kevin http://n4.nabble.com/file/n996068/trainDescr.txt trainDescr.txt
 http://n4.nabble.com/file/n996068/trainY.txt trainY.txt
 --
 View this message in context: 
 http://n4.nabble.com/Please-help-me-Error-in-data-frame-x-retained-drop-FALSE-undefined-columns-selected-tp996068p996068.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.




-- 

Max

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Ordering variables in a parallel coordinates plot

2010-01-02 Thread Tal Galili

Hello all,

I am searching for a way in R to re-order variables before presenting them
in a parallel coordinates plot.

So far I didn't find anything within a R related context on how to do this.
I did find some texts talking about how it should be done in general, here
is such example:
http://tinyurl.com/ycnsjpe

Is there a package or an example of the variable ordering (for parallel
coordinate plot) in R ?

Thanks,
Tal


Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com/ (English)
--

[[alternative HTML version deleted]]

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

[R] Rscript: how to suppress all output

How can I suppress ALL output when running Rscript in Terminal?

~/DocumentsRscript test.r

I tried options --slave, --vanilla with no success. I get these

Loading required package: methods
..etc..

and other output as well.

-J

 sessionInfo()
R version 2.9.2 (2009-08-24)
i386-apple-darwin8.11.1

locale:
fi_FI.UTF-8/fi_FI.UTF-8/C/C/fi_FI.UTF-8/fi_FI.UTF-8

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

other attached packages:
[1] ggplot2_0.8.3   reshape_0.8.3   plyr_0.1.9  proto_0.3-8
Hmisc_3.7-0 survival_2.35-7

loaded via a namespace (and not attached):
[1] cluster_1.12.1  lattice_0.17-26


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Re: [R] suppress output for meta in package tm

2010-01-02 Thread Amber Jaycocks

Thanks Jim and Peter.  Ignoring the filename worked.  The process is still
slow but a bit improved.  I had to slightly modify the substring to match
across the two objects.

n_corp_file - capture.output(meta(corpa[[n]], URI),file=)
n_char - nchar(n_corp_file[1])
n_char_dir - nchar(corpa_dir)
# want to start at file(\ = 6 + directory + 2
corp_file -substr(n_corp_file, 6+ n_char_dir +2, n_char-3)
corp_file - corp_file[1]

##this doesnt suppress, but works too
#n_corp_file - meta(corpa[[n]], URI)
##want just file not dir and file
#n_char - nchar(n_corp_file[2])
##nchar[1] is file=4 and nchar[2] is dir + filename amd nchar[3] is
UTF-8 = 5
#n_char_dir - nchar(corpa_dir)
#corp_file - substr(n_corp_file, n_char_dir + 2, n_char)
#corp_file - corp_file[2]
#END of nonsupressed

On Sat, Jan 2, 2010 at 11:19 AM, jim holtman jholt...@gmail.com wrote:

 Actually if you just use 'capture.output' without specifying a 'file' it
 will return a character vector with the output which you can just ignore.

   On Sat, Jan 2, 2010 at 1:51 PM, Peter Ehlers ehl...@ucalgary.ca wrote:

  I don't know anything about pkg:tm, but I'll make a
 couple of comments below.


 Amber Jaycocks wrote:

 Hi, Peter.

 Thanks.  This works but is not ideal to have an external file.  The main
 reason I want to suppress the output is to speed up the processing time,
 which capture.output does indeed do.  It is a great work around for now.

 I am using the output to match items in a corpa to a file that contains
 metadata and then attaching the fields in the meta data file as metadata
 to
 each item in the corpa.  If you have any other suggestions to increase
 processing speed please let me know.  Many Thanks.

 for (n in 1:length(corpa)) {

 or: for(n in seq_along(corpa)){


 n_corp_file - capture.output(meta(corpa[[n]], URI),file=log.txt)

 here, I think, you want:
 capture.output(n_corp_file - meta(corpa[[n]], URI), file=log.txt)

 and I would use (on Windows): file=clipboard


 #want just file not dir and file
 n_char - nchar(n_corp_file[2])
 #nchar[1] is file=4 and nchar[2] is dir + filename amd nchar[3] is
 UTF-8
 = 5
 n_char_dir - nchar(corpa_dir)
 corp_file - substr(n_corp_file, n_char_dir + 2, n_char)
 corp_file - corp_file[2]
 #match corpa file with meta data file
 match_index - match(corp_file,(meta_data$file))
 if (!is.na(match_index)) {
 #attach all rows of meta_data
 meta_cols - colnames(meta_data)
 for (col in 1:length(meta_cols)) {
 meta(corpa[[n]], meta_cols[col]) - meta_data[match_index,meta_cols[col]]
 }
 } #if
 } #for n corpa


 You might also find sink() to be more to your taste than
 capture.output().

  -Peter


 On Sat, Jan 2, 2010 at 6:03 AM, Peter Ehlers ehl...@ucalgary.ca wrote:

 Can you wrap your call in capture.output(..., file=...)?

  -Peter Ehlers

 Amber Jaycocks wrote:

  Hello,

 I am using the tm package and wish to suppress the output for meta.  I
 am
 defining another variable for one of the tags and don't want the value
 printed on the screen.  Any help would be appreciated.  Thanks.

 here is the commnad:

 n_corp_file - meta(corpa[[n]], URI)

 -Amber

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 --
 Peter Ehlers
 University of Calgary
 403.202.3921



 --
 Peter Ehlers
 University of Calgary
 403.202.3921

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




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

 What is the problem that you are trying to solve?


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

Re: [R] Rscript: how to suppress all output