labdsv (version 1.8-0)

dsvdis: Dissimilarity Indices and Distance Measures

Description

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.

Usage

dsvdis(x,index,weight=rep(1,ncol(x)),step=0.0,
       diag=FALSE, upper=FALSE)

Arguments

x

a matrix of observations, samples as rows and variables as columns

index

a specific dissimilarity or distance index (see details below)

weight

a vector of weights for species (columns)

step

a threshold dissimilarity to initiate shortest-path adjustment (0.0 is a flag for no adjustment)

diag

a switch to control returning diagonal (default=FALSE)

upper

a switch to control returning upper (TRUE) or lower (FALSE) triangle

Value

Returns an object of class "dist", equivalent to that from dist.

Details

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	\(1 - a / \sqrt{(a+b) \times (a+c)}\)

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 allow 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 "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".

References

http://ecology.msu.montana.edu:/labdsv/R/labs/lab8/lab8.html

See Also

dist, vegdist

Examples

# NOT RUN {
    data(bryceveg)   # returns a data.frame called "bryceveg"
    dis.ochiai <- dsvdis(bryceveg,index="ochiai")
    dis.bc <- dsvdis(bryceveg,index="bray/curtis")
# }