Thanks! it worked great.
Much appreciated.
Brian
On 11/8/2010 5:44 PM, Jacob van Etten wrote:
> Oops, the function should of course be something like this:
>
> func <- function(x)
>
>
> {
>
>
> from <- c(12,1:11)[x[13]]
>
>
> to <- c(2:12,1)[x[13]]
>
>
> return(sum(x[c(from,x[13],to)]))
>
>
> }
>
> --- On *Mon, 8/11/10, Jacob van Etten /<jacobvanet...@yahoo.com>/* wrote:
>
>
> From: Jacob van Etten <jacobvanet...@yahoo.com>
> Subject: Re: [R-sig-Geo] Bioclimatic variables - wettest quarter
> To: "Brian Oney" <zenli...@gmail.com>
> Cc: r-sig-geo@stat.math.ethz.ch
> Date: Monday, 8 November, 2010, 16:58
>
> Hi Brian,
>
>
>
>
>
> Something strange is going on. Normally, this should produce a stack.
>
>
>
>
>
> This works, for instance:
>
>
>
>
>
> fn <- system.file("external/test.grd", package="raster")
>
>
> s <- stack(fn, fn)
>
>
> t <- calc(s, function(x) x*10)
>
>
> plot(t)
>
>
>
>
>
> I think something strange is going on with your stack. Try some
> basic operations on it like
>
>
>
>
>
> plot(mon_stac * 10)
>
>
>
>
>
> to see what´s going on. Also, check if you have the latest version
> of raster, etc.
>
>
>
>
>
> Regarding your question what to do with the output you get with my
> suggestion: well, it can be used to index the temperature raster to
> retrieve the values you want. You can append the index raster to the
> temperature raster
>
>
>
>
>
> s <- stack(mon_temp, wettest_quarter)
>
>
>
>
>
> and then use calc() with a function like this (assuming you took
> the middle month, type="around", not type="from"):
>
>
>
>
>
> func <- function(x)
>
>
> {
>
>
> from <- c(12,1:11)[x[13]]
>
>
> to <- c(2:12,1)[x[13]]
>
>
> return(mean(x[from:to]))
>
>
> }
>
>
>
> overlay() should also work, but you get these ugly functions with
> 12 arguments!
>
>
>
>
> Best,
>
>
>
>
>
> Jacob.
>
> --- On Mon, 8/11/10, Brian Oney <zenli...@gmail.com
> </mc/compose?to=zenli...@gmail.com>> wrote:
>
> From: Brian Oney <zenli...@gmail.com
> </mc/compose?to=zenli...@gmail.com>>
> Subject: Re: [R-sig-Geo] Bioclimatic variables - wettest quarter
> To: "Jacob van Etten" <jacobvanet...@yahoo.com
> </mc/compose?to=jacobvanet...@yahoo.com>>
> Cc: r-sig-geo@stat.math.ethz.ch
> </mc/compose?to=r-sig-...@stat.math.ethz.ch>
> Date: Monday, 8 November, 2010, 14:48
>
>
>
>
>
>
> Hi Jacob,
>
> Thanks for the suggestion. So...
>
>
>
> func <- function(X) {x <- movingFun(c(X), n=3, sum, 'from',
> circular=TRUE);return(x)}
>
> mon_stac <- stack(paste(pc_clim,"",y,"_prec",1:12,".asc",
> sep=""))
>
> # then
>
> wetness_quarters <- calc(mon_stac, func)
>
> Error in .local(x, fun, ...) : function 'fun' returns more
> than one
> value
>
>
>
> # This make sense that this would do this..
>
> # Now this to get the first month of the max quarter by returning
> first month number:
>
> func <- function(X) {x <- which.max(movingFun(c(X), n=3, sum,
> 'from', circular=TRUE));return(x)}
>
>
>
> # Then
>
> wetness_quarters <- calc(mon_stac, func)
>
> Error in v[, tr$row[i]:(tr$row[i] + tr$nrows[i] - 1)] <-
> matrix(sv, nrow = ncol(outraster)) :
>
> incorrect number of subscripts on matrix
>
> # This error being returned after a long time busying a quadcore
> computer...
>
>
>
> Even if I can get your suggestion to work, I am still faced
> with the
> problem of retrieving the sum of values of the quarter marked
> my the
> month number,
>
> which should look something like this:
>
>
>
> quart_value <- function(a,b,d,e,f,g,i,j,k,l,m,n,o){
>
> ifelse(o==1, X <- mean(c(a,b,d)),
>
> ifelse(o==2, X <- mean(c(b,d,e)),
>
> ifelse(o==3, X <- mean(c(d,e,f)),
>
> ifelse(o==4, X <- mean(c(e,f,g)),
>
> ifelse(o==5, X <- mean(c(f,g,i)),
>
> ifelse(o==6, X <- mean(c(g,i,j)),
>
> ifelse(o==7, X <- mean(c(i,j,k)),
>
> ifelse(o==8, X <- mean(c(j,k,l)),
>
> ifelse(o==9, X <- mean(c(k,l,m)),
>
> ifelse(o==10, X <- mean(c(l,m,n)),
>
> ifelse(o==11, X <- mean(c(m,n,a)),
>
> ifelse(o==12, X <-
> mean(c(n,a,b)),NA))))))))))))
>
> return(X)}
>
>
>
> #For BIO8
>
> mon_stac.wq <- stack(paste(pc_clim,"",y,"_tmean",1:12,".asc",
> sep=""), wetness_quarters)
>
> tmean.wq <- overlay(mon_stac.wq, fun=quart_value)
>
>
>
> With "o" being the product of the "func"or "maxmonth" function
>
> I think that I NEED to get the "overlay" function to work, but
> am of
> course open to suggestions.
>
> I appreciate the help.
>
>
>
> Regards,
>
> Brian
>
>
>
>
>
> On 11/8/2010 10:59 AM, Jacob van Etten wrote:
>
>
>
>
> I don´t know what
> the problem is with overlay(), but you could use an
> alternative approach, using calc() instead.
>
>
>
> Something like this (not tried)
>
>
>
> library(raster)
>
> library(dismo)
>
> func <- function(x, ...) movingFun(x, n=3, sum,
> circular=TRUE)
>
> wetness_quarters <- calc(mon_stac, func)
>
> wettest_quarter <- calc(wetness_quarters, function(x)
> which(x == max(x))
>
>
>
> The output input should indicate the month in the centre
> of the wettest quarter.
>
>
>
> Jacob.
>
>
>
> --- On Mon, 8/11/10, Brian Oney <zenli...@gmail.com
> </mc/compose?to=zenli...@gmail.com>>
> wrote:
>
>
>
> From: Brian Oney <zenli...@gmail.com
> </mc/compose?to=zenli...@gmail.com>>
>
> Subject: [R-sig-Geo] Bioclimatic variables - wettest
> quarter
>
> To: r-sig-geo@stat.math.ethz.ch
> </mc/compose?to=r-sig-...@stat.math.ethz.ch>
>
> Date: Monday, 8 November, 2010, 1:40
>
>
>
> Hello All,
>
>
>
> I am attempting to reproduce the bioclimatic
> (Worldclim, Hijmans et al
>
> 2005) variables with the raster package and I am
> stuck
> on the group
>
> "temp of driest quarter" etc. variables.
>
> I am attempting it with the function "overlay"
> ("raster" package).
>
>
>
> Here is how it looks:
>
> # To know the first month of the wettest quarter
>
> maxmonth<- function(a,b,d,e,f,g,i,j,k,l,m,n){
>
> o<- sum(c(a,b,d))
>
> p<- sum(c(b,d,e))
>
> r<- sum(c(d,e,f))
>
> u<- sum(c(e,f,g))
>
> v<- sum(c(f,g,i))
>
> w<- sum(c(g,i,j))
>
> x<- sum(c(i,j,k))
>
> y<- sum(c(j,k,l))
>
> z<- sum(c(k,l,m))
>
> aa<- sum(c(l,m,n))
>
> ab<- sum(c(m,n,a))
>
> ac<- sum(c(n,a,b))
>
> ad<-
> which.max(c(o,p,r,u,v,w,x,y,z,aa,ab,ac))
>
> return(ad)}
>
> >
>
> maxmonth(a=13,b=16,d=41,e=61,f=41,g=16,i=15,j=14,k=13,l=11,m=31,n=11)
>
> # works: 2nd element (month) is the beginning of the
> wettest quarter
>
> [1] 2
>
> mon_stac<-
> stack(paste(pc_clim,"",y,"_prec",1:12,".asc",
> sep=""))
>
> # Now attempt it
>
> avg<- overlay(mon_stac, fun=maxmonth)
>
> Error in .overlayList(rasters, fun = fun, filename =
> filename, ...) :
>
> cannot use this formula; lenghts do not match
>
>
>
> # How about manually?
>
> a<- raster(paste(pc_clim,"",y,"_prec",1,".asc",
> sep=""))
>
> b<- raster(paste(pc_clim,"",y,"_prec",2,".asc",
> sep=""))
>
> d<- raster(paste(pc_clim,"",y,"_prec",3,".asc",
> sep=""))
>
> e<- raster(paste(pc_clim,"",y,"_prec",4,".asc",
> sep=""))
>
> f<- raster(paste(pc_clim,"",y,"_prec",5,".asc",
> sep=""))
>
> g<- raster(paste(pc_clim,"",y,"_prec",6,".asc",
> sep=""))
>
> i<- raster(paste(pc_clim,"",y,"_prec",7,".asc",
> sep=""))
>
> j<- raster(paste(pc_clim,"",y,"_prec",8,".asc",
> sep=""))
>
> k<- raster(paste(pc_clim,"",y,"_prec",9,".asc",
> sep=""))
>
> l<- raster(paste(pc_clim,"",y,"_prec",10,".asc",
> sep=""))
>
> m<- raster(paste(pc_clim,"",y,"_prec",11,".asc",
> sep=""))
>
> n<- raster(paste(pc_clim,"",y,"_prec",12,".asc",
> sep=""))
>
>
>
> avg<- overlay(a,b,d,e,f,g,i,j,k,l,m,n,
> fun=maxmonth)
>
> Error in .overlayList(rasters, fun = fun, filename =
> filename, datatype
>
> = datatype, :
>
> cannot use this formula; lenghts do not match
>
>
>
> Also doesn't work...
>
> > length(mon_stac[1])
>
> [1] 12
>
> I have 12 rasters being fed into overlay, but it
> won't
> buy it.
>
> I think that my first step is to know the first
> month
> of the wettest
>
> month. Once I can do that I can do it for
> temperature
> as well.
>
>
>
> Thanks and Regards,
>
> Brian
>
>
>
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>
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