This function provides a set of alternative dissimilarity indices and distance metrics for classification and ordination, including weighting by species (columns) and shortest-path adjustment for dissimilarity indices.
dsvdis(x,index,weight=rep(1,ncol(x)),step=0.0,
diag=FALSE, upper=FALSE)Returns an object of class "dist", equivalent to that from dist.
a matrix of observations, samples as rows and variables as columns
a specific dissimilarity or distance index (see details below)
a vector of weights for species (columns)
a threshold dissimilarity to initiate shortest-path adjustment (0.0 is a flag for no adjustment)
a switch to control returning the diagonal (default=FALSE)
a switch to control returning the upper (TRUE) or lower (FALSE) triangle
David W. Roberts droberts@montana.edu
The function calculates dissimilarity or distance between rows of a matrix of observations according to a specific index. Three indices convert the data to presence/absence automatically. In contingency table notation, they are:
| steinhaus | \(1 - a / (a + b + c)\) |
| sorensen | \(1 - 2a / (2a + b +c)\) |
| ochiai | \(1 - a / \sqrt{(a+b) * (a+c)}\) |
Others are quantitative. For variable i in samples x and y:
| ruzicka | \(1 - \sum \min(x_i,y_i) / \sum \max(x_i,y_i)\) |
| bray/curtis | \(1 - \sum[2 * \min(x_i,y_i)] / \sum x_i + y_i\) |
| roberts | \(1 - [(x_i+y_i) * \min(x_i,y_i) / \max(x_i,y_i)] / (x_i + y_i)\) |
| chisq | \((exp - obs) / \sqrt{exp}\) |
The weight argument allows the assignment of weights to individual species in the calculation of plot-to-plot similarity. The weights can be assigned by life-form, indicator value, or for other investigator specific reasons. For the presence/absence indices the weights should be integers; for the quantitative indices the weights should be in the interval [0,1]. The default (rep(1,ncol(x)) is to set all species = 1.
The threshold dissimilarity ‘step’ sets all values greater than or equal to "step" to 9999.9 and then solves for the shortest path distance connecting plots to other non-9999.9 values in the matrix. Step = 0.0 (the default) is a flag for "no shortest-path correction".
dist, vegdist
data(bryceveg) # returns a data.frame called "bryceveg"
dis.ochiai <- dsvdis(bryceveg,index="ochiai")
dis.bc <- dsvdis(bryceveg,index="bray/curtis")
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