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 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo