Dear Liusfo and Jean, Thank you both for your help and suggestions, which both work.
As Jean mentioned, there is no real speed up using the apply family, which I thought there would be, so I will stick with the for loop for clarity. Liusfo, the reason I used c(1,2) in the apply function (i.e. mask_data <- apply(data,c(1,2),mask,y=lsmask)) was because this is what you would do if you wanted to sum all the two-dimensional vectors over time (for instance to produce an average of a field over a year). i.e. to get the sum you would do sum_data <- apply(data,c(1,2),sum) I thought it would extend to using my mask function. Anyway, thanks again for both of your help. Cheers, Justin -- Justin Peter Research Fellow International Centre for Applied Climate Sciences, University of Southern Queensland West St, Toowoomba, QLD, 4350 Australia Email: justin.pe...@usq.edu.au<mailto:justin.pe...@usq.edu.au> Ph: +61 (0) 7 4631 1181 Fax: +61 (0) 7 4631 5581 Mob: +61 (0)474 774 107 -----Original Message----- From: Luisfo <luisf...@yahoo.es<mailto:luisfo%20%3cluisf...@yahoo.es%3e>> To: "Adams, Jean" <jvad...@usgs.gov<mailto:%22Adams,%20jean%22%20%3cjvad...@usgs.gov%3e>>, Justin Peter <justin.pe...@usq.edu.au<mailto:justin%20peter%20%3cjustin.pe...@usq.edu.au%3e>> CC: r-help@r-project.org <r-help@r-project.org<mailto:%22r-h...@r-project.org%22%20%3cr-h...@r-project.org%3e>> Subject: Re: [R] Using apply on a three dimensional matrix and passing multiple arguments to user defined function Date: Wed, 7 Sep 2016 16:05:48 +0200 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.pe...@usq.edu.au><mailto:justin.pe...@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.pe...@usq.edu.au<mailto:justin.pe...@usq.edu.au><mailto:justin.pe...@usq.edu.au><mailto:justin.pe...@usq.edu.au> Ph: +61 (0) 7 4631 1181 Fax: +61 (0) 7 4631 5581 Mob: +61 (0)474 774 107 _____________________________________________________________ This email (including any attached files) is confidential and is for the intended recipient(s) only. If you received this email by mistake, please, as a courtesy, tell the sender, then delete this email. The views and opinions are the originator's and do not necessarily reflect those of the University of Southern Queensland. Although all reasonable precautions were taken to ensure that this email contained no viruses at the time it was sent we accept no liability for any losses arising from its receipt. 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The University of Southern Queensland is a registered provider of education with the Australian Government. (CRICOS Institution Code QLD 00244B / NSW 02225M, TEQSA PRV12081 ) [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
