Compute a Functional Dissimilarity Matrix

Source: R/compute_dist_matrix.R

Wrapper for cluster::daisy() function in cluster package, to compute distance matrix of trait between each pair of species present in given traits_table, each row represents a species and each column a trait. To be able to compute other metrics traits_table must have species name as row names.

compute_dist_matrix(
  traits_table,
  metric = "gower",
  center = FALSE,
  scale = FALSE
)

Arguments

traits_table

a data.frame of traits with species in row and traits in columns, row names should be species names,

metric

character vector in list 'gower', 'manhattan', 'euclidean' defining the type of distance to use (see cluster::daisy()), see Details section,

center

logical that defines if traits should be centered (only in the case of 'euclidean' distance)

scale

logical that defines if traits should be scaled (only in the case of 'euclidean' distance)

Value

A functional distance matrix, column and row names follow species name from traits_table row names.

Details

The functional distance matrix can be computed using any type of distance metric. When traits are both quantitative and qualitative Gower's (Gower, 1971; Podani, 1999) distance can be used. Otherwise, any other distance metric (Euclidean, Manhattan, Minkowski) can be used - as long as the rows and the columns are named following the species. When using mixed data consider also Gower's distance extension by Pavoine et al. (2009). IMPORTANT NOTE: in order to get functional rarity indices between 0 and 1, the distance metric has to be scaled between 0 and 1.

References

Gower, J.C. (1971) A general coefficient of similarity and some of its
properties. Biometrics, 857–871.

Podani, J. (1999) Extending Gower’s general coefficient of similarity
to ordinal characters. Taxon, 331–340.

Pavoine, S., Vallet, J., Dufour, A.-B., Gachet, S., & Daniel, H. (2009)
On the challenge of treating various types of variables: application for
improving the measurement of functional diversity. Oikos, 118, 391–402.

See also

cluster::daisy() which this function wraps, base stats::dist() or ade4::dist.ktab() for Pavoine et al. (2009) extension of Gower's distance.

Examples

set.seed(1)  # For reproducibility
trait = data.frame(
   sp = paste("sp", 1:5),
   trait_1 = runif(5),
   trait_2 = as.factor(c("A", "A", "A", "B", "B")))

rownames(trait) = trait$sp

dist_mat = compute_dist_matrix(trait[, -1])