How can I write 3 blocks of code to 3 files when the blocks of code and the file names are in different lists

General
2

I'm not sure I understand exactly what you're trying to do, and unfortunately the code example is not easily reproducible since it involves reading in files that aren't created by the code. Could you please turn this question into a reprex?

I'm especially unsure about what you mean by "merging" the files in the sublists. The code is using merge(), but if all the files have the same variables, this doesn't make much sense. Do you maybe mean instead that you want to row-bind the imported data frames (like stacking them on top of each other)?

Here's one example of how you might do what I think you're trying to do. It's very possible that I've misunderstood your problem, so the details of how you want to combine the files in the sublists might be wrong. Still, the general approach should work even if those details change. This is also an example of how you can make a reprex that involves reading and writing files.

# Setup example files and file lists
in_dir <- paste0(tempdir(), "/in_files")
out_dir <- paste0(tempdir(), "/out_files")

dir.create(in_dir)
dir.create(out_dir)

for (x in 1:9) {
  write.table(
    warpbreaks[(x * 3):((x * 3) + 2), ], 
    file = paste0(file.path(in_dir, "warpbreaks_"), x, ".txt"),
    sep = "\t",
    quote = FALSE,
    row.names = FALSE
  )
}

file_list1 <- as.list(paste0("warpbreaks_", 1:4, ".txt"))
file_list2 <- as.list(paste0("warpbreaks_", 5:7, ".txt"))
file_list3 <- as.list(paste0("warpbreaks_", 8:9, ".txt"))

file_lists <- list(file_list1, file_list2, file_list3)
file_lists
#> [[1]]
#> [[1]][[1]]
#> [1] "warpbreaks_1.txt"
#> 
#> [[1]][[2]]
#> [1] "warpbreaks_2.txt"
#> 
#> [[1]][[3]]
#> [1] "warpbreaks_3.txt"
#> 
#> [[1]][[4]]
#> [1] "warpbreaks_4.txt"
#> 
#> 
#> [[2]]
#> [[2]][[1]]
#> [1] "warpbreaks_5.txt"
#> 
#> [[2]][[2]]
#> [1] "warpbreaks_6.txt"
#> 
#> [[2]][[3]]
#> [1] "warpbreaks_7.txt"
#> 
#> 
#> [[3]]
#> [[3]][[1]]
#> [1] "warpbreaks_8.txt"
#> 
#> [[3]][[2]]
#> [1] "warpbreaks_9.txt"


# Import and bind together files in each sublist, then output with new names
new_names <- c("name1.txt", "name2.txt", "name3.txt")

new_dfs <- lapply(
  file_lists,
  function(lst) {
    df_lst <- lapply(
      lst,
      function(fl) { read.table(file.path(in_dir, fl), header = TRUE) }
    )
   do.call(what = rbind, args = df_lst)
  }
)

new_dfs
#> [[1]]
#>    breaks wool tension
#> 1      54    A       L
#> 2      25    A       L
#> 3      70    A       L
#> 4      52    A       L
#> 5      51    A       L
#> 6      26    A       L
#> 7      67    A       L
#> 8      18    A       M
#> 9      21    A       M
#> 10     29    A       M
#> 11     17    A       M
#> 12     12    A       M
#> 
#> [[2]]
#>   breaks wool tension
#> 1     18    A       M
#> 2     35    A       M
#> 3     30    A       M
#> 4     36    A       M
#> 5     36    A       H
#> 6     21    A       H
#> 7     24    A       H
#> 8     18    A       H
#> 9     10    A       H
#> 
#> [[3]]
#>   breaks wool tension
#> 1     43    A       H
#> 2     28    A       H
#> 3     15    A       H
#> 4     26    A       H
#> 5     27    B       L
#> 6     14    B       L

for (index in seq_along(new_dfs)) {
  write.table(
    new_dfs[[index]], 
    file = file.path(out_dir, new_names[[index]]), 
    sep = "\t", quote = FALSE, row.names = FALSE
  )
}

list.files(out_dir, full.names = TRUE)
#> [1] "/tmp/RtmpxLmJym/out_files/name1.txt"
#> [2] "/tmp/RtmpxLmJym/out_files/name2.txt"
#> [3] "/tmp/RtmpxLmJym/out_files/name3.txt"

# `reprex()` can't run this line, but it can be run by hand
if(interactive()) {
  file.show(list.files(out_dir, full.names = TRUE))
}

Created on 2018-08-21 by the reprex package (v0.2.0).

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