Dear list: I am trying to get pixel-wise correlations and significance between two raster bricks; one representing monthly NDVI means and another representing monthly rainfall means.
I found the following two codes (both from Robert Hijmans) from a previous discussions on this list: http://r-sig-geo.2731867.n2.nabble.com/questions-on-RasterStack-Brick-td5553580.html and from StackOverflow: http://stackoverflow.com/questions/16698048/r-calculating-pearson-correlation-coefficient-in-each-cell-along-time-line # code 1 > funcal <- function(xy) { > xy <- na.omit(matrix(xy, ncol=2)) > if (ncol(xy) < 2) { > NA > } else { > cor(xy[, 1], xy[, 2]) > } > } > s <- stack(sa, sb) > calc(s, funcal) > # code 2 > stackcor <- function(s1, s2, method='spearman') { > mycor <- function(v) { > x <- v[1:split] > y <- v[(split+1):(2*split)] > cor(x, y, method=method) > } > s <- stack(s1, s2) > split <- nlayers(s)/2 > calc(s, fun=mycor ) > } Both codes work as expected with the "cor" function, producing correlation grids. However, I tried substituting the cor with cor.test in order to extract the p-values: # using the first code > funcal <- function(xy) { > xy <- na.omit(matrix(xy, ncol=2)) > if (ncol(xy) < 2) { > NA > } else { > cor.test(xy[, 1], xy[, 2],method="pearson")$p.value > } > } > s <- stack(sa, sb) > calc(s, funcal) I am met with the following error (with trackback in RStudio): Error in cor.test.default(xy[, 1], xy[, 2], method = "pearson") : > not enough finite observations > 8 stop("not enough finite observations") > 7 cor.test.default(xy[, 1], xy[, 2], method = "pearson") > 6 cor.test(xy[, 1], xy[, 2], method = "pearson") > 5 FUN(newX[, i], ...) > 4 apply(v, 1, fun) > 3 .local(x, fun, ...) > 2 calc(meistack, brick.cor.pval) > 1 calc(meistack, brick.cor.pval) In the previous r-sig-geo, a user had asked about this error but it was left unanswered. I was wondering if anyone can help with this? Thanks! Hakim ____________________________________________________ Hakim Abdi | PhD Candidate Geobiosphere Science Center Department of Physical Geography and Ecosystem Science Lund University, Sölvegatan 12, SE-223 62 Lund, Sweden Email: hakim.a...@nateko.lu.se [[alternative HTML version deleted]]
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