Question

A very unexpected behavior of the useful data.frame in R arises from keeping character columns as factor. This causes many problems if it is not considered. For example suppose the following code:

foo=data.frame(name=c("c","a"),value=1:2)
#   name val
# 1    c   1
# 2    a   2

bar=matrix(1:6,nrow=3)
rownames(bar)=c("a","b","c")
#   [,1] [,2]
# a    1    4
# b    2    5
# c    3    6

Then what do you expect of running bar[foo$name,]? It normally should return the rows of bar that are named according to the foo$name that means rows ‘c’ and ‘a’. But the result is different:

bar[foo$name,]
#   [,1] [,2]
# b    2    5
# a    1    4

The reason is here: foo$name is not a character vector, but an integer vector.

foo$name
# [1] c a
# Levels: a c

To have the expected behavior, I manually convert it to character vector:

foo$name = as.character(foo$name)
bar[foo$name,]
#   [,1] [,2]
# c    3    6
# a    1    4

But the problem is that we may easily miss to perform this, and have hidden bugs in our codes. Is there any better solution?

Answer 1

This is a feature and R is working as documented. This can be dealt with generally in a few ways:

1. use the argument stringsAsFactors = TRUE in the call to data.frame(). See ?data.frame

2. if you detest this behaviour so, set the option globally via

   options(stringsAsFactors = FALSE)
   

3. (as noted by @JoshuaUlrich in comments) a third option is to wrap character variables in I(....). This alters the class of the object being assigned to the data frame component to include "AsIs". In general this shouldn’t be a problem as the object inherits (in this case) the class "character" so should work as before.

You can check what the default for stringsAsFactors is on the currently running R process via:

> default.stringsAsFactors()
[1] TRUE

The issue is slightly wider than data.frame() in scope as this also affects read.table(). In that function, as well as the two options above, you can also tell R what all the classes of the variables are via argument colClasses and R will respect that, e.g.

> tmp <- read.table(text = '"Var1","Var2"
+ "A","B"
+ "C","C"
+ "B","D"', header = TRUE, colClasses = rep("character", 2), sep = ",")
> str(tmp)
'data.frame':   3 obs. of  2 variables:
 $ Var1: chr  "A" "C" "B"
 $ Var2: chr  "B" "C" "D"