[R] Efficiency question: replacing all NAs with a zero

[Dimitri Liakhovitski]

Just tried it. It's definitely faster - but I get the same error:
" Reached total allocation of 1535Mb:"

On Mon, Mar 29, 2010 at 8:27 PM, Gabor Grothendieck
<ggrothendieck at gmail.com> wrote:
> 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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>> and provide commented, minimal, self-contained, reproducible code.
>>
>



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