R help - Sep 2007 - NAs in indices

Hi All,

I'm fiddling with an program to read a text file containing periods that
SAS uses for missing values. I know that if I had the original SAS data
set instead of a text file, R would handle this conversion for me. 

Data frames do not allow missing values in their indices but vectors do.
Why is that? A search of the error message points out the problem and
solution but not why they differ. A simplified program that demonstrates
the issue is below.

Thanks,
Bob

# Here's a data frame that has both periods and NAs.
# I want sex to remain character for now.

sex=c("m","f",".",NA)
x=c(1,2,3,NA)
myDF <- data.frame(sex,x,stringsAsFactors=F)
rm(sex,x)
myDF

# Substituting NA into data frame does not work
# due to NAs in the indices. The error message is:
# missing values are not allowed in subscripted assignments of data
frames

myDF[ myDF$sex==".", "sex" ] <- NA
myDF

# This works because myDF$sex is a vector and vectors allow NAs in
indexes.
# Why don't data frames allow this?

myDF$sex[ myDF$sex=="." ] <- NA
myDF

========================================================Bob Muenchen (pronounced
Min'-chen), Manager
Statistical Consulting Center
U of TN Office of Information Technology
200 Stokely Management Center, Knoxville, TN 37996-0520
Voice: (865) 974-5230 
FAX: (865) 974-4810
Email: muenchen at utk.edu
Web: http://oit.utk.edu/scc, 
News: http://listserv.utk.edu/archives/statnews.html

On Sun, 2 Sep 2007, Muenchen, Robert A (Bob) wrote:
> Hi All,
>
> I'm fiddling with an program to read a text file containing periods
that
> SAS uses for missing values. I know that if I had the original SAS data
> set instead of a text file, R would handle this conversion for me.
>
> Data frames do not allow missing values in their indices but vectors do.
> Why is that? A search of the error message points out the problem and
> solution but not why they differ. A simplified program that demonstrates
> the issue is below.
>
> Thanks,
> Bob
>
> # Here's a data frame that has both periods and NAs.
> # I want sex to remain character for now.
>
> sex=c("m","f",".",NA)
> x=c(1,2,3,NA)
> myDF <- data.frame(sex,x,stringsAsFactors=F)
> rm(sex,x)
> myDF
>
> # Substituting NA into data frame does not work
> # due to NAs in the indices. The error message is:
> # missing values are not allowed in subscripted assignments of data
> frames
>
> myDF[ myDF$sex==".", "sex" ] <- NA
> myDF
>
> # This works because myDF$sex is a vector and vectors allow NAs in
> indexes.
> # Why don't data frames allow this?
>
> myDF$sex[ myDF$sex=="." ] <- NA
> myDF

R version 2.5.1  'allows' it.

> df <- as.data.frame(diag(3)[,-1])
> df[ df[,1]==1 ] <- NA
> df
but the result may not be what you were expecting. See

 	 ?"[.data.frame"

(esp. Details) for more info on why it does not 'work' as you expected.


Also, since you mention a 'text file' I suggest you look at

 	 ?read.table

or

 	?scan

where you will see that

 	dots.are.NA <- read.table("my.file", na.strings = '.' )

may help you.

Chuck
>
> ========================================================> Bob Muenchen
(pronounced Min'-chen), Manager
> Statistical Consulting Center
> U of TN Office of Information Technology
> 200 Stokely Management Center, Knoxville, TN 37996-0520
> Voice: (865) 974-5230
> FAX: (865) 974-4810
> Email: muenchen at utk.edu
> Web: http://oit.utk.edu/scc,
> News: http://listserv.utk.edu/archives/statnews.html
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

Muenchen, Robert A (Bob) wrote:
> Hi All,
> 
> I'm fiddling with an program to read a text file containing periods
that
> SAS uses for missing values. I know that if I had the original SAS data
> set instead of a text file, R would handle this conversion for me. 
> 
> Data frames do not allow missing values in their indices but vectors do.
> Why is that? A search of the error message points out the problem and
> solution but not why they differ. A simplified program that demonstrates
> the issue is below.
> 
> Thanks,
> Bob
> 
> # Here's a data frame that has both periods and NAs.
> # I want sex to remain character for now.
> 
> sex=c("m","f",".",NA)
> x=c(1,2,3,NA)
> myDF <- data.frame(sex,x,stringsAsFactors=F)
> rm(sex,x)
> myDF
> 
> # Substituting NA into data frame does not work
> # due to NAs in the indices. The error message is:
> # missing values are not allowed in subscripted assignments of data
> frames
> 
> myDF[ myDF$sex==".", "sex" ] <- NA
> myDF
> 
Hi Bob,
What happens is that you don't get FALSE when you ask if something==NA, 
you get NA. However, if you use the "which" function, it cleans up the
NAs for you and the result of that should do what you want.

myDF[which(myDF$sex=="."),"sex"]<-NA

Jim