[R-sig-Geo] Comparing 2 rasterbricks using functions from TSdist package

[Jackson Rodrigues]

Dear all,

Few days ago I got a important help from this list and I am really thankful
for that.
Today I have a similar challenge with 2 rasterbrick files.

I would like to compare 2 rasterbricks using any similarity function (let's
take CorDistance) from package TSdist.
In my real data, both rasterbricks came from the same region but using
different measurement techniques.

I am trying to adapt the suggestion I got from here rather than looping on
each cell, but no matter what I try I always get an error related to NA.
It seems to be very simples but I am stuck since last Monday.

I have played with several conditional ("ifelse", "if", "if else" etc) and
logical tests ("|", "||", "&" etc) but I got nothing so far.

Could someone help me and show me a path to go through?
Below there is the cleanest code I have tried.

Best regards

Jackson

##############
library(raster)
library(TSdist)

set.seed(12)
r <- raster(nrow=10, ncol=10)
s <- lapply(1:200, function(i) setValues(r, rnorm(ncell(r),
                                                  sample.int(5,1), 0.5)))
s <- stack(s)
s[s < 0] <- NA
s2<-s^2

# Visualize that some pixels have NAs and other don't
hasna <- stackApply(s, indices = 1, fun = function(x, na.rm){anyNA(x)})
hasna2 <- stackApply(s2, indices = 1, fun = function(x, na.rm){anyNA(x)})

par(mfrow=c(1,2))
plot(hasna);plot(hasna2)

# CorDistance function does not handle NAs
CorDistance(as.vector(s[1]),as.vector(s2[1]))
[1] 0.2192382

CorDistance(as.vector(s[2]),as.vector(s2[2]))
<simpleError in .common.ts.sanity.check(x): NA in the series>
  [1] NA

fun <- function(x,y){
  out <- ifelse(anyNA(x) | anyNA(y),
                yes = NA,
                no = unname(CorDistance(x,y)))
  return(out)
}

# Check that it works
fun(as.vector(s[1]),as.vector(s2[1]))
[1] 0.2192382

# Check that it does not work
fun(as.vector(s[2]),as.vector(s2[2]))
[1] NA

new_s1 <- fun(s,s2)
<simpleError in if (any(is.na(x))) { stop("NA in the series")}:
  argument is not interpretable as logical>

# Check that it does not work with calc
new_s2 <- calc(s,s2, fun = fun)
Error in .calcTest(x[1:5], fun, na.rm, forcefun, forceapply) :
  cannot use this function

plot(s_out)
#############

-- 

Jackson M. Rodrigues

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