[R] Using apply on a three dimensional matrix and passing multiple arguments to user defined function

[Luisfo]

Hi,

Jean's example with lapply works fine.

However, if you still want to use apply, I think this works.
One observation first. You were passing c(1,2) as second argument to 
apply, in your code. And that is what makes you have lots of NAs as a 
result, since your function is being applied twice, by rows and columns 
(first and second dimensions) respectively.
Use:
     masked_data <- apply(data,3,mask,y=lsmask)
     # but now masked_data has dim(nlon*nlat,ntime), so change it
     dim(masked_data) <- dim(data)

The apply goes over the third dimension (second parameter '3'), so it 
takes every nlot*nlat matrix as first argument for function mask.
I think it should work.

Regards,

*Luisfo Chiroque*
/PhD Student | PhD Candidate
IMDEA Networks Institute/
http://fourier.networks.imdea.org/people/~luis_nunez/ 
<http://fourier.networks.imdea.org/people/%7Eluis_nunez/>

On 09/07/2016 03:17 PM, Adams, Jean wrote:
> Justin,
>
> I don't think you can get the apply() function to return an array.  You
> could use lapply() instead, and then use simplify2array() to convert the
> list of matrices to an array.  Also, in your mask() function you don't need
> the which() and you should return the x.  See my example with toy data
> below.
>
> # toy data
> nlon <- 2
> nlat <- 4
> ntime <- 3
> data <- array(1:(nlon*nlat*ntime), dim=c(nlon, nlat, ntime))
> lsmask <- array(sample(0:1, size=nlon*nlat, replace=TRUE), dim=c(nlon,
> nlat))
>
> # newly defined function
> mask <- function(x, y) {
>    x[y==0] <- NA
>    x
> }
>
> # doit
> data2 <- simplify2array(lapply(1:ntime, function(i) mask(data[, , i],
> lsmask)))
>
>
> You may prefer to stick with the for() loop approach (for clarity or
> simplicity or ...)  When I ramped up the toy data to much larger
> dimensions, the lapply() approach was only slightly faster than the for()
> loop approach on my PC.
>
> data3 <- data
> data3[ , , i] <- mask(data3[ , , i], lsmask)
>
> Jean
>
>
>
>
> On Tue, Sep 6, 2016 at 11:33 PM, Justin Peter <Justin.Peter at usq.edu.au>
> wrote:
>
>> Dear R-user,
>>
>> I have a three-dimensional matrix of atmospheric data. The first two
>> dimensions are spatial (lon and lat) and the third is time, such that
>>
>> dim(data) <- c(nlon,nlat,ntime)
>>
>> I wish to apply a land sea mask data which is a matrix of "0" and "1" if
>> dim(nlon,nlat)
>>
>> dim(lsmask) <- c(nlon,nlat)
>>
>> I wish to set all of the elements in the two-dimensional array of
>> data[,,ntime] for every 1:length(ntime).
>>
>> I could do this in a loop:
>>
>> for (i in 1:ntime){
>>      data[,,i][which(lsmask == 0)] <- NA
>> }
>>
>> I would like to do this using apply, but I need to pass two variables to
>> the function in apply (data and lsmask), where data is a two-dimensional
>> array.
>>
>> I tried:
>>
>> mask <- function(x,y) {x[which(y==0)] <- NA}
>>
>> masked_data <- apply(data,c(1,2),mask,y=lsmask)
>>
>> but I get back a vector of dim(nlon,nlat) populated with NA.
>>
>> Any clues as to what I am missing?
>>
>> Thanks in advance for you help.
>>
>> Kind regards,
>> Justin
>>
>>
>>
>> --
>> Justin Peter
>> Research Fellow
>> International Centre for Applied Climate Sciences,
>> University of Southern Queensland
>> West St, Toowoomba, QLD, 4350
>> Australia
>>
>> Email: justin.peter at usq.edu.au<mailto:justin.peter at usq.edu.au>
>> Ph: +61 (0) 7 4631 1181
>> Fax: +61 (0) 7 4631 5581
>> Mob: +61 (0)474 774 107
>>
>>
>>
>>
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