Hi Jacob,
You are right it does produce a stack. I did not know that calc can
handle a computation like that for stack, impressive.
So I have tried your suggestions and hate to keep bothering but it still
is not completely working, but we are making progress:
func <- function(X) {x <- movingFun(c(X), n=3, sum, "around",
circular=TRUE);return(x)}
wetness_quarters <- calc(mon_stac, func)
# It worked!
summary(wetness_quarters)
#Error in cbind(sum...@values, as.matrix(sm)) :
# number of rows of matrices must match (see arg 2)
str(wetness_quarters) # looks ok
wettest_quarter <- calc(wetness_quarters, function(x) which(x == max(x)))
#Error in setValues(out, x) : values must be numeric, integer or logical.
wettest_quarter <- calc(wetness_quarters, which.max)
#Error in .local(x, values) : values must be numeric, integer or logical.
Could it be that I have way too many places that have only NA values?
i.e. NA values over the ocean?
?which.max tells me that NA's are discarded.
I know it is UGLY. I just didn't have a better idea, and I would have
never dreamed up your proposed function. I am a little green, but I
really appreciate the help.
Cheers,
Brian
On 11/8/2010 4:58 PM, Jacob van Etten wrote:
> 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 /<[email protected]>/* wrote:
>
>
> From: Brian Oney <[email protected]>
> Subject: Re: [R-sig-Geo] Bioclimatic variables - wettest quarter
> To: "Jacob van Etten" <[email protected]>
> Cc: [email protected]
> 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 /<[email protected]>
>> </mc/[email protected]>/* wrote:
>>
>>
>> From: Brian Oney <[email protected]>
>> </mc/[email protected]>
>> Subject: [R-sig-Geo] Bioclimatic variables - wettest quarter
>> To: [email protected]
>> </mc/[email protected]>
>> 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
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [email protected]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>
[[alternative HTML version deleted]]
_______________________________________________
R-sig-Geo mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
