xdistance {ecodist} R Documentation

## Cross-distance between two datasets.

### Description

Pairwise dissimilarity calculation between rows of one dataset and rows of another, for instance across different sampling periods for the same set of sites.

### Usage

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 method used there, currently: "euclidean", "bray-curtis", "manhattan", "mahalanobis" (squared Mahalanobis distance), "jaccard", "difference", "sorensen", "gower", "modgower10" (modified Gower, base 10), "modgower2" (modified Gower, base 2). Partial matching will work for selecting a method.

### 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.

### Value

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

distance, xmantel, xmgram

### Examples

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))


[Package ecodist version 2.0.9 Index]