Question

It seems that I do not understand the nested for loop well enough. I am trying to work with multiple directories in a nested for loop something like this:

    sp_folder1<-list.files("species1/",full.names=TRUE)
    sp_folder2<-list.files("species2/",full.names=TRUE)
setwd(sp_folder1)
    for(i in 1: length(sp_folder1)){
      for(j in 1: length(sp_folder2){
         sp_i<-read.delim(list.files(sp_folder1)[i],header=T)
    sp_j<-read.delim(list.files(sp_folder2)[j],header=T)
    Do something with both files
         }
      }

but, I am getting an error:
Error in file (file, ‘rt’): cannot open the connection
no such file or directory:
Though, the first file from ‘sp_folder1’ is fine. I tried not setting the working directory as well but still it did not work.

Answer 1

The easiest way would be to read the files prior to the loop. I assume that you have two subdirectories which hold the files.

(Code not tested)

#create vectors of filenames
#I assume that this works for you
sp_folder1<-list.files("species1/",full.names=TRUE)
sp_folder2<-list.files("species2/",full.names=TRUE)

#set working directory
setwd('.../species1')
#loop over filenames, read all files and put the data.frames in a list
dat.list.1 <- lapply(sp_folder1,read.delim,header=TRUE)
setwd('.../species2')
dat.list.2 <- lapply(sp_folder2,read.delim,header=TRUE)

Now you have two lists of data.frames, which you can access in your loops using, e.g., dat.list.1[[i]].