From eriki at ccbr.umn.edu  Tue Jun 29 22:41:57 2010
From: eriki at ccbr.umn.edu (Erik Iverson)
Date: Tue, 29 Jun 2010 15:41:57 -0500
Subject: [Rd] read.table / type.convert with NA values
Message-ID: <4C2A5A95.6060104@ccbr.umn.edu>

Hello,

While assisting a fellow R-helper off list, I narrowed down an issue he 
was having to the following behavior of type.convert, called through 
read.table.  This is using R 2.10.1, if newer versions don't exhibit 
this behavior, apologies.

# generates numeric vector
 > type.convert(c("123.42", "NA"))
[1] 123.42     NA

# generates a numeric vector, notice the space before 123.42
 > type.convert(c(" 123.42 ", "NA"))
[1] 123.42     NA

# generates factor, notice the space before NA
# note that the 2nd element is actually " NA", not a true NA value
 > type.convert(c("123.42", " NA"))
[1] 123.42  NA
Levels: 123.42  NA


How can this affect read.table/read.csv use 'in the wild'?

This gentleman had a data file that was

1) delimited by something other than white space, CSV in his case
2) contained missing values, designated by NA in his case
3) contained white space between delimiters and data values, e.g.,

NA,     NA,    4.5,    NA

as opposed to

NA,NA,4.5,NA


With these 3 conditions met, read.table gives type.convert a character 
vector like my third example above, and ultimately he got a data.frame 
consisting of only factors when we were expecting numeric columns.  This 
was easily fixed either by modifying the read.csv function call to 
specify colClasses directly, or in his case, strip.white = TRUE did the 
job just fine.

I believe the confusion stems from the fact that with no NA values in 
our data file, this would work as we would expect.  The introduction of 
what we thought were NA values changed the behavior.  In reality, these 
were not being treated as NA values by read.table/type.convert.  The 
question is, should they be in this case?

This behavior of read.table/type.convert may very well be what is 
expected/needed.  If so, this note could still be of use to someone in 
the future if they stumble upon similar behavior.  The fact I wasn't 
able to uncover anyone who asked about it on list before probably means 
the situation is rare.

Best Regards,
Erik Iverson



[Rd] read.table / type.convert with NA values
Erik Iverson