[R-sig-eco] for loop - list.files()

[Daniel Gruner]

Hi:

Back in 2007 I wrote code to loop through & open 1000 separate text 
files (species-sample incidence (0,1) matrices, from 1000 null model 
simulation runs), extract key information from each of the files, and 
paste append each result as a row in an output matrix.

This worked fine in 2007, but for some reason it is not working now. 
I wonder if there have been some changes in the commands I use in the 
chunk, such that I now have to modify the code accordingly. I am not 
attaching data because I would need to send along a bunch of txt 
files to place in a directory, but if you are interested in running 
this I can send everything to you (or a manageable subset).

The error I receive is:
"Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") : cannot open file 'Sim1.txt': No such file or directory"

And here is the code (again, it worked just fine for multiple users 
in 2007!). I get the same error when I run just the read.table() line 
but for what reason I cannot divine.

###
# this creates a character string of all the 1000 text files stored 
in a directory, alone, with no other files
PlantSims <- list.files(path="C:/user/directory")
# create temporary matrix that to store the summary data from 17 
islands in each run; clear it (below) for next run
result <- matrix(0,nrow=17,ncol=1)

# loop through and open each of the text files in the list 
"PlantSims", calculate, drop result for
# 17 islands as 1 of 1000 rows in file="output.txt"
# "incidence" is the total no. islands (of 17) a species is found
for (i in 1:length(PlantSims)) {
tmp<-read.table(PlantSims[i],row.names=1,header=T, sep=" ")
incidence <- rowSums(tmp)
for (j in 1:ncol(tmp)) {
	for (i in 1:nrow(tmp)) {
		if((tmp[i,j] == 1) & (incidence[i] == 1)) result[j,1] <- result[j,1] + 1.0
                }
        }
cat(t(result), file = "output.txt", sep = " ", fill = TRUE, labels = 
FALSE, append = TRUE)
result <- matrix(0,nrow=17,ncol=1)
}
###

What might be wrong with this loop, specifically, with the 
read.table() statement, and is there a better way? The first 
"PlantSims" statement works correctly, so I do not know why 
read.table() cannot handle it within the loop.

Thanks very much in advance,


Daniel S. Gruner, Assistant Professor
Department of Entomology
4112 Plant Sciences Bldg
University of Maryland
College Park, MD 20742 U.S.A.
(o) 301-405-3957  (f) 301-314-9290
dsgruner at umd.edu

http://grunerlab.umd.edu