[R] Problem with Tinn-R communicating with REvolution R
I have been using Tinn-R with R without any problems but when I try to use it with REvolution R I get the following error message when Tinn-R runs the configuration script and gets to the trDDEInstall() function: ## Start DDE trDDEInstall() trDDEInstall() Error in structure(.External(dotTcl, ..., PACKAGE = tcltk), class = tclObj) : [tcl] invalid command name dde. In addition: Warning message: In tclRequire(dde, warn = TRUE) : Tcl package 'dde' not found I have not found anything about this on the Tinn-R forum and have had no repsonse from the REvolution R forum. I have checked other R-Help queries but these relate to adding the code for .trPaths which I already have. Does anyone know how to solve this problem? [[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.
[R] Tinn-R RGui Send problem
A possible work around would be to append the selection.r file to the .RHistory file and then reload the history, e.g. file.append(.Rhistory, .trPaths[5]) loadhistory(file= .Rhistory) You can then access the code on the console, skipping the last 2 lines. [[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] Tinn-R RGui Send problem
A possible work around would be to append the selection.r file to the .Rhistory file and then reload the history, e.g. file.append(.Rhistory, .trPaths[5]) loadhistory(file= .Rhistory) You can then access the code on the console, skipping the last 2 lines. [[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] Fwd: R apply() help -urgent
Set up a function for the fisher.test on a 2x2 table and then include
this in the apply function for columns as in the example below. The
result is a list with names A to Z
# set up a dummy data set with 100 rows
Cat-LETTERS[sample(1:6,100, replace=T)]
GL-sample(1:6, 100, replace=T)
dat-matrix(sample(c(0,1),100*27, replace=T), nrow=100)
colnames(dat)-c(LETTERS[1:26],pLoss)
data1-data.frame(Cat, GL, dat)
# define function fro fisher.test
ff-function(x,y){
fisher.test(table(x,y))
}
# apply function to columns A to Z
results-apply(data1[,LETTERS[1:26]],2, ff, y=data1[,pLoss])
# the results are in the form of a list with names A to Z
results$C
On 19:59, Venkatesh Patel wrote:
-- Forwarded message --
From: Dr. Venkateshdrve...@liv.ac.uk
Date: Sun, May 9, 2010 at 4:55 AM
Subject: R apply() help -urgent
To: r-help@r-project.org
I have a file with 4873 rows of 1s or 0s and has 26 alphabets (A-Z) as
columns. the 27th column also has 1s and 0s but stands for a different
variable (pLoss). columns 1 and 2 are not significant and hence lets ignore
them for now.
here is how the file looks
CatGL A B C D E F G H I J K L M N O P Q
R S T U V W X Y Z pLoss
H 5 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
E 5 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
P 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 1
P 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 1
F 6 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
E 4 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
H 5 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
J 4 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
J 4 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
E 5 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
S 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 1 0 0 0 0 0 0 0 1
..
..
..
..
..
..
Alphabets A-Z stand for different categories of protein families and pLoss
stands for their presence or absence in an animal.
I intend to do Fisher's test for 26 individual 2X2 tables constructed from
each of these alphabets vs pLoss.
For example, here is what I did for alphabet A and then B and then C so
on. (I have attached R-input.csv for your perusal)
data1- read.table(R_input.csv, header = T)
datatable- table(data1$A, data1$pLoss) #create a new datatable2 or 3
with table(data1$B.. or (data1$C.. and so on
datatable
01
0 31 4821
10 21
now run the Fisher's test for these datatables one by one for the 26
alphabets :(
fisher.test(datatable), ... fisher.test(datatable2)...
in this case, the task is just for 26 columns.. so I can do it manually.
But I would like to do an automated extraction and fisher's test for all the
columns.
I tried reading the tutorials and trying a few examples. Cant really come up
with anything sensible.
How can I use apply() in this regard? or is there any other way, a loop may
be? to solve this issue.
Please help.
Thanks a million in advance,
Dr Venkatesh Patel
School of Biological Sciences
University of Liverpool
United Kingdom
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[R] Problem with Sweave not recognising \Sexpr{}
I am trying to run the Sweave example at
http://www.stat.uni-muenchen.de/~leisch/Sweave/Sweave-Rnews-2002-3.pdf
However, the \Sexpr{} code is not being evaluated, although the actual R
code within the {} runs ok in R.
Below is part of the resulting .tex file. Can anyone help identify the
cause? I am using R 2.10.1 on Windows XP.
Consider the \texttt{cats} regression example from Venables \ Ripley
(1997). The data frame contains measurements of heart and body weight
of \Sexpr{nrow(cats)} cats (\Sexpr{sum(cats$Sex==F)} female,
\Sexpr{sum(cats$Sex==M)} male).
Thanks
Mike White
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with Sweave not recognising \Sexpr{}
I think I have solved the problem. In the Sweave manual it mentions that
problems may occur after loading the R2HTML package. I have not
recently loaded this package but the proposed solution to problems
caused by R2HTML also solves my problem with the evaluation of R code in
\Sexpr. It seems that it is necessary to set the syntax option in the
Sweave function as follows
Sweave(..., syntax=SweaveSyntaxNoweb)
although I am not sure why this is required.
Mike
On 19:59, Mike White wrote:
I am trying to run the Sweave example at
http://www.stat.uni-muenchen.de/~leisch/Sweave/Sweave-Rnews-2002-3.pdf
However, the \Sexpr{} code is not being evaluated, although the actual
R code within the {} runs ok in R.
Below is part of the resulting .tex file. Can anyone help identify
the cause? I am using R 2.10.1 on Windows XP.
Consider the \texttt{cats} regression example from Venables \ Ripley
(1997). The data frame contains measurements of heart and body weight
of \Sexpr{nrow(cats)} cats (\Sexpr{sum(cats$Sex==F)} female,
\Sexpr{sum(cats$Sex==M)} male).
Thanks
Mike White
__
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.
