Using sep = "." in `fread` from "data.table"

Question

Can fread from "data.table" be forced to successfully use "." as a sep value?

I'm trying to use fread to speed up my concat.split functions in "splitstackshape". See this Gist for the general approach I'm taking, and this question for why I want to make the switch.

The problem I'm running into is treating a dot (".") as a value for sep. Whenever I do so, I get an "unexpected character" error.

The following simplified example demonstrates the problem.

library(data.table)

y <- paste("192.168.1.", 1:10, sep = "")

x1 <- tempfile()
writeLines(y, x1)
fread(x1, sep = ".", header = FALSE)
# Error in fread(x1, sep = ".", header = FALSE) : Unexpected character (
# 192) ending field 2 of line 1

The workaround I have in my current function is to substitute "." with another character that is hopefully not present in the original data, say "|", but that seems risky to me since I can't predict what is in someone else's dataset. Here's the workaround in action.

x2 <- tempfile()
z <- gsub(".", "|", y, fixed=TRUE)
writeLines(z, x2)
fread(x2, sep = "|", header = FALSE)
#      V1  V2 V3 V4
#  1: 192 168  1  1
#  2: 192 168  1  2
#  3: 192 168  1  3
#  4: 192 168  1  4
#  5: 192 168  1  5
#  6: 192 168  1  6
#  7: 192 168  1  7
#  8: 192 168  1  8
#  9: 192 168  1  9
# 10: 192 168  1 10

For the purposes of this question, assume that the data are balanced (each line will have the same number of "sep" characters). I'm aware that using a "." as a separator is not the best idea, but I'm just trying to account for what other users might have in their datasets, based on other questions I've answered here on SO.

Answer 1

Now implemented in v1.9.5 on GitHub.

> input = paste( paste("192.168.1.", 1:5, sep=""), collapse="\n")
> cat(input,"\n")
192.168.1.1
192.168.1.2
192.168.1.3
192.168.1.4
192.168.1.5 

Setting sep='.' results in ambiguity with the new argument dec (by default '.') :

> fread(input,sep=".")
Error in fread(input, sep = ".") : 
  The two arguments to fread 'dec' and 'sep' are equal ('.')

Therefore choose something else for dec :

> fread(input,sep=".",dec=",")
    V1  V2 V3 V4
1: 192 168  1  1
2: 192 168  1  2
3: 192 168  1  3
4: 192 168  1  4
5: 192 168  1  5

You may get a warning :

> fread(input,sep=".",dec=",")
     V1  V2 V3 V4
 1: 192 168  1  1
 2: 192 168  1  2
 3: 192 168  1  3
 4: 192 168  1  4
 5: 192 168  1  5
Warning message:
In fread(input, sep = ".", dec = ",") :
  Run again with verbose=TRUE to inspect... Unable to change to a locale
  which provides the desired dec. You will need to add a valid locale name
  to getOption("datatable.fread.dec.locale"). See the paragraph in ?fread.

Either ignore or suppress the warning, or read the paragraph and set the option :

options(datatable.fread.dec.locale = "fr_FR.utf8")

This ensures there can be no ambiguity.