Claddis (version 0.7.0)

calculate_MPD: Calculate mean pairwise distances

Description

Given distanceMatrices and taxonGroups objects calculates their mean pairwise distances.

Usage

calculate_MPD(distances, taxon_groups)

Value

A labelled vector of weighted mean pairwise distances.

Arguments

distances

An object of class distanceMatrices.

taxon_groups

An object of class taxonGroups.

Author

Graeme T. Lloyd

Details

Not all measures of disparity (morphological distance) require an ordination space. For example, the pariwise distances between taxa are themselves a disparity metric. This function takes the output from calculate_morphological_distances and a set of taxon groups and returns the mean pairwise distance for each of those groups.

Examples

# Get morphological distances for the Day et al. (2016) data set:
distances <- calculate_morphological_distances(
  cladistic_matrix = day_2016,
  distance_metric = "mord",
  distance_transformation = "none"
)

# Build simple taxonomic groups for Day et al. (2016) data set:
taxon_groups <- list(nonBurnetiamorpha = c("Biarmosuchus_tener", "Hipposaurus_boonstrai",
  "Bullacephalus_jacksoni", "Pachydectes_elsi", "Niuksenitia_sukhonensis", "Ictidorhinus_martinsi",
  "RC_20", "Herpetoskylax_hopsoni"), Burnetiamorpha = c("Lemurosaurus_pricei", "Lobalopex_mordax",
  "Lophorhinus_willodenensis", "Proburnetia_viatkensis", "Lende_chiweta",
  "Paraburnetia_sneeubergensis", "Burnetia_mirabilis", "BP_1_7098"))

# Set class as taxonGroups:
class(taxon_groups) <- "taxonGroups"

# Calculate mean pairwise distances:
calculate_MPD(distances, taxon_groups)