For a while, I have been using the setwd() command at the beginning of a project's code. This allows one to save data, graph, output easily to a project's result folder without typing long path names.

Yesterday, I was using a contributed package in R that requires the access to R's temp directory. The exact location of this folder can be found out using the command tempdir(). It just happened that my current location of this folder was not ideal for the task at hand and I needed to change it. There was no command in R to change it. I figured out a way to do it: add an entry to the environmental variable list of the system as TMPDIR and specify the desired folder name.

## Tuesday, November 13, 2007

## Monday, November 12, 2007

### Useful websites for graphics in R

R graphical manuals (a nice collection of examples and codes)

http://cged.genes.nig.ac.jp/RGM2/index.php?clear=all

Codes from the book "R graphics"

http://www.stat.auckland.ac.nz/~paul/RGraphics/rgraphics.html

http://cged.genes.nig.ac.jp/RGM2/index.php?clear=all

Codes from the book "R graphics"

http://www.stat.auckland.ac.nz/~paul/RGraphics/rgraphics.html

## Friday, November 02, 2007

### Fast permuting r by c two-way tables

Today, I need to permute

I also made a function to do the permutation for each line of my huge

matrix and used the apply() function to speed up things. It works pretty well

for me.

*many*two-way tables of the same dimension (say 2 by 3) to carry out a test of independence. My data looks like a big matrix with each row corresponding to a two-way table (arranged by row). The permutation is just to draw a random 2 by 3 table given independence between the two dimensions, conditioning on the observed marginal distributions. I didn't find (or didn't have time to find) a function to do that in R. Therefore I wrote the following codes:f.perm.tab<-function(x){

x.r<-rep(1:nrow(x), times=rowSums(x))

x.c<-rep(1:ncol(x), times=colSums(x))

temp.mat<-expand.grid(1:nrow(x), 1:ncol(x))

return(table(c(x.r, temp.mat[,1]), c(sample(x.c),temp.mat[,2])) -matrix(1, nrow(x), ncol(x)))

}

I also made a function to do the permutation for each line of my huge

matrix and used the apply() function to speed up things. It works pretty well

for me.

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