Preventing column-class inference in fread()

Question

Is there a way for fread to mimic the behaviour of read.table whereby the class of the variable is set by the data that is read in.

Answer 1

Option 1: Using a system command

fread() allows the use of a system command in its first argument. We can use it to remove the quotes in the first column of the file.

indt <- data.table::fread("cat test.csv | tr -d '\"'", nrows = 100)
str(indt)
# Classes ‘data.table’ and 'data.frame':    100 obs. of  2 variables:
#  $ x: int  1 2 3 4 5 6 7 8 9 10 ...
#  $ y: int  1 2 3 4 5 6 7 8 9 10 ...
#  - attr(*, ".internal.selfref")= 

The system command cat test.csv | tr -d '\"' explained:

• cat test.csv reads the file to standard output
• | is a pipe, using the output of the previous command as input for the next command
• tr -d '\"' deletes (-d) all occurrences of double quotes ('\"') from the current input

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Option 2: Coercion after reading

Since option 1 doesn't seem to be working on your system, another possibility is to read the file as you did, but convert the x column with type.convert().

library(data.table)
indt2 <- fread("test.csv", nrows = 100)[, x := type.convert(x)]
str(indt2)
# Classes ‘data.table’ and 'data.frame':    100 obs. of  2 variables:
#  $ x: int  1 2 3 4 5 6 7 8 9 10 ...
#  $ y: int  1 2 3 4 5 6 7 8 9 10 ...
#  - attr(*, ".internal.selfref")= 

Side note: I usually prefer to use type.convert() over as.numeric() to avoid the "NAs introduced by coercion" warning triggered in some cases. For example,

x <- c("1", "4", "NA", "6")
as.numeric(x)
# [1]  1  4 NA  6
# Warning message:
# NAs introduced by coercion 
type.convert(x)
# [1]  1  4 NA  6

But of course you can use as.numeric() as well.

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Note: This answer assumes data.table dev v1.9.5