xdistance {ecodist} | R Documentation |
Pairwise dissimilarity calculation between rows of one dataset and rows of another, for instance across different sampling periods for the same set of sites.
xdistance(x, y, method = "euclidean")
x |
A site by species or other matrix or data frame. |
y |
A a second site by species dataset, which must have at least the same columns. |
method |
This function calls |
This function will calculate rowwise dissimilarities between any pair of matrices or data frames with the same number of columns. Note that the cross-dissimilarity functions are for research purposes, and are not well-tested.
A non-symmetric and possibly not square matrix of dissimilarities of class xdist
, where result <- xdistance(x, y)
produces a matrix with result[a, b]
containing the dissimilarity between x[a, ]
and y[b, ]
.
Sarah Goslee
data(graze) ### EXAMPLE 1: Square matrices # take two subsets of sites with different dominant grass abundances # use cut-offs that produce equal numbers of sites dom1 <- subset(graze, POPR > 50 & DAGL < 20) # 8 sites dom2 <- subset(graze, POPR < 50 & DAGL > 20) # 8 sites # first two columns are site info dom.xd <- xdistance(dom1[, -c(1,2)], dom2[, -c(1,2)], "bray") # environmental and spatial distances; preserve rownames forest.xd <- xdistance(dom1[, "forestpct", drop=FALSE], dom2[, "forestpct", drop=FALSE]) sitelocation.xd <- xdistance(dom1[, "sitelocation", drop=FALSE], dom2[, "sitelocation", drop=FALSE]) # permutes rows and columns of full nonsymmetric matrix xmantel(dom.xd ~ forest.xd) xmantel(dom.xd ~ forest.xd + sitelocation.xd) plot(xmgram(dom.xd, sitelocation.xd)) ### EXAMPLE 2: Non-square matrices # take two subsets of sites with different dominant grass abundances # this produces a non-square matrix dom1 <- subset(graze, POPR > 45 & DAGL < 20) # 13 sites dom2 <- subset(graze, POPR < 45 & DAGL > 20) # 8 sites # first two columns are site info dom.xd <- xdistance(dom1[, -c(1,2)], dom2[, -c(1,2)], "bray") # environmental and spatial distances; preserve rownames forest.xd <- xdistance(dom1[, "forestpct", drop=FALSE], dom2[, "forestpct", drop=FALSE]) sitelocation.xd <- xdistance(dom1[, "sitelocation", drop=FALSE], dom2[, "sitelocation", drop=FALSE]) # permutes rows and columns of full nonsymmetric matrix xmantel(dom.xd ~ forest.xd, dims=c(13, 8)) xmantel(dom.xd ~ forest.xd + sitelocation.xd, dims=c(13, 8)) plot(xmgram(dom.xd, sitelocation.xd))