Hi folks,
I am trying to recurse through several numbered subfolders in a directory. Each
folder has many trees 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,
library(ape)
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$edge.length)
branchdata.5 <- rbind(branchdata.5, iteration.edges.5)
}
The problem comes when I want to iterate through the numbered subdirectories
while also iterating through the files in a given directory. I want to
recursively assign these data frames as well, with something like
f <- list.dirs(path = "/.../.../etc", full.names = FALSE, recursive = FALSE)
for (j in 1:length(f)) {
setwd(paste("/.../.../.",j,sep=""))
assign( paste("branchdata.5",j,sep=""), data.frame() )
iterations <- as.character(c(1:length(trees)))
for (i in 1:iters) {
tree <- read.tree(trees[i])
assign(paste("iteration.edges.5",j,sep=""), as.numeric(tree$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 = "")
}
The problem seems to be in the rbind() when using values with assign() and
paste(). I would love some help on this!
John S. S. Denton
Ph.D. Candidate
Department of Ichthyology and Richard Gilder Graduate School
American Museum of Natural History
www.johnssdenton.com
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