# Cross-distance between two datasets. Pairwise dissimilarity calculation between rows of one dataset and rows of another, for instance across different sampling periods for the same set of sites. ```r xdistance(x, y, method = "euclidean") ``` ## Arguments - `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 `distance` to do the calculations, and will accept any symmetric method used there, currently: "euclidean", "bray-curtis", "manhattan", "mahalanobis" (squared Mahalanobis distance), "jaccard", "sorensen", "gower", "modgower10" (modified Gower, base 10), "modgower2" (modified Gower, base 2). Partial matching will work for selecting a method. The asymmetric "difference" method will not work for calculating cross-distances. ## Details 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. ## Returns 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, ]`. ## Author(s) Sarah Goslee ## See Also `distance`, `xmantel`, `xmgram` ## Examples ```r 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)) ```

xdistance function