R help - Mar 2010 - Efficiency question: replacing all NAs with a zero

Dear R'ers,

I have a very large data frame (over 4000 rows and 2,500 columns). My
task is very simple - I have to replace all NAs with a zero. My code
works fine on smaller data frames - but I have to deal with a huge one
and there are many NAs in each column.
R runs out of memory on me ("Reached total allocation of 1535Mb: see
help(memory.size)"). Is there any other, more efficient way of doing
it?
Thanks a lot for any hints!
Dimitri


# Building an example frame:
frame<-data.frame(a=rnorm(1:100),b=rnorm(1:100),c=rnorm(1:100),d=rnorm(1:100),e=rnorm(1:100),f=rnorm(1:100),g=rnorm(1:100))
set.seed(1234)
for(i in names(frame)){
	i.for.NA<-sample(1:100,60)
	frame[[i]][i.for.NA]<-NA
}

# Replacing all NAs in "frame" with zeros - is of course fast in this
example, because this data frame is very small
system.time({
frame<-lapply(frame,function(x){
	x[is.na(x)]<-0
	return(x)
})})


-- 
Dimitri Liakhovitski
Ninah.com
Dimitri.Liakhovitski at ninah.com

See if this works for you:

DF[is.na(DF)] <- 0

On Mon, Mar 29, 2010 at 8:21 PM, Dimitri Liakhovitski <ld7631 at
gmail.com> wrote:
> Dear R'ers,
>
> I have a very large data frame (over 4000 rows and 2,500 columns). My
> task is very simple - I have to replace all NAs with a zero. My code
> works fine on smaller data frames - but I have to deal with a huge one
> and there are many NAs in each column.
> R runs out of memory on me ("Reached total allocation of 1535Mb: see
> help(memory.size)"). Is there any other, more efficient way of doing
> it?
> Thanks a lot for any hints!
> Dimitri
>
>
> # Building an example frame:
>
frame<-data.frame(a=rnorm(1:100),b=rnorm(1:100),c=rnorm(1:100),d=rnorm(1:100),e=rnorm(1:100),f=rnorm(1:100),g=rnorm(1:100))
> set.seed(1234)
> for(i in names(frame)){
> ? ? ? ?i.for.NA<-sample(1:100,60)
> ? ? ? ?frame[[i]][i.for.NA]<-NA
> }
>
> # Replacing all NAs in "frame" with zeros - is of course fast in
this
> example, because this data frame is very small
> system.time({
> frame<-lapply(frame,function(x){
> ? ? ? ?x[is.na(x)]<-0
> ? ? ? ?return(x)
> })})
>
>
> --
> Dimitri Liakhovitski
> Ninah.com
> Dimitri.Liakhovitski at ninah.com
>
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