R loop opening files - r

Question

I am trying to run a simple 5 lines command but over 9000 different files. I wrote the following for loop
setwd("/Users/morandin/Desktop/Test")
output_file<- ("output_file.txt")
files <- list.files("/Users/morandin/Desktop/Test")
for(i in files) {
chem.w.in <- scan(i, sep=",")
pruned.tree<-drop.tip(mytree,which(chem.w.in %in% NA))
plot(pruned.tree)
pruned.tree.ja.chem.w.in <- phylo4d(pruned.tree, c(na.omit(chem.w.in)))
plot(pruned.tree.ja.chem.w.in)
out <- abouheif.moran(pruned.tree.ja.chem.w.in)
print(out)
}
Hey I am editing my question: the above code does the for loop perfectly now (thanks for all your help). I am still having an issue with the output.
I can redirect the entire output using R through bash commands but I would need the name of the processed file. My output looks like this:
class: krandtest
Monte-Carlo tests
Call: as.krandtest(sim = matrix(res$result, ncol = nvar, byrow = TRUE),
obs = res$obs, alter = alter, names = test.names)
Number of tests: 1
Adjustment method for multiple comparisons: none
Permutation number: 999
Test Obs Std.Obs Alter Pvalue
1 dt 0.1458514 0.7976225 greater 0.2
other elements: adj.method call
Is there a way to print Pvalue results and name of the file (element i)??
Thanks

Answer 1

Since Paul Hiemstra's answer answered #1, here's an answer to #2, assuming that by "answers" you mean "the printed output of abouheif.moran(pruned.tree.ja.chem.w.in)".
Use cat() with the argument append = true. For example:
output_file = "my_output_file.txt"
for(i in files) {
# do stuff
# make plots
out <- abouheif.moran(pruned.tree.ja.chem.w.in)
out <- sprintf("-------\n %s:\n-------\n%s\n\n", i, out)
cat(out, file = output_file, append = TRUE)
}
This will produce a file called my_output_file.txt that looks like:
-------
file_1:
-------
output_goes_here
-------
file_2:
-------
output_goes_here
Obviously the formatting is entirely up to you; I just wanted to demonstrate what could be done here.
An alternative solution would be to sink() the entire script, but I'd rather be explicit about it. A middle road might be to sink() just a small piece of the code, but except in extreme cases it's a matter of preference or style.

Answer 2

I suspect what is going wrong here is that list.files() by default returns a list of only the names of the files, not the entire path to the file. Setting full.names to TRUE will fix this issue. Note that you will not have to add the txt add the filename as list.files() already returns the full path to an existing file.