R help - Apr 2012 - assign() and paste() for data.frame() in nested for loops

Hi folks,

I am trying to recurse through several subfolders in a directory. Each
folder has many entries that I want to display summary values for. I have
been expanding data frames using code with the structure name <- rbind(name,
newvals) to produce a data frame with n rows equal to the number of files in
one of the folders, and n column equal to the number of values in the file.

I can loop over the values within a single subdirectory fine with, for
example, 

trees <- list.files(pattern="*.tre")
iters=length(trees)

branchdata.5 <- data.frame()

iterations <- as.character(c(1:length(trees)))

for (i in 1:iters) {

tree <- read.tree(trees[i])
iteration.edges.5 <- as.numeric(tree$edge.length)

branchdata.5 <- rbind(branchdata.5, iteration.edges.5)

} 

The problem comes when I want to iterate through the subdirectories while
also iterating through the files in a given directory. I want to recursively
assign these data frames as well, with something like

f <- list.dirs(path = "/.../.../etc", full.names = FALSE, recursive
= FALSE)

for (j in 1:length(f)) {

setwd(paste("/.../.../.",j,sep=""))

assign( paste("branchdata.5",j,sep=""), data.frame() )

iterations <- as.character(c(1:length(trees)))

for (i in 1:iters) {

tree <- read.tree(trees[i])
assign(paste("iteration.edges.5",j,sep=""),
as.numeric(tree$edge.length) )

paste("branchdata.5",j,sep="") <-
rbind(paste("branchdata.5",j,sep=""),
paste("iteration.edges.5",j,sep=""))

}

names(iterations) <- NULL
boxplot(t(paste("branchdata.5",j,sep="")) , horizontal=TRUE
,
names=iterations , ylim=c(0,2), xlab="Branch Lengths" ,
ylab="Iterations" ,
main = "GTR + indels")

}

The problem seems to be in the rbind() when using values with assign() and
paste(). I would love some help on this!

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