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

[Adams, Jean]

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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