calculate_MPD: Calculate mean pairwise distances

In graemetlloyd/Claddis: Measuring Morphological Diversity and Evolutionary Tempo

Calculate mean pairwise distances

Description

Given distanceMatrices and taxonGroups objects calculates their mean pairwise distances.

Usage

calculate_MPD(distances, taxon_groups)

Arguments

distances	An object of class distanceMatrices.
taxon_groups	An object of class taxonGroups.

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.

Value

A labelled vector of weighted mean pairwise distances.

Author(s)

Graeme T. Lloyd [e-mail]

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)

graemetlloyd/Claddis documentation built on May 9, 2024, 8:07 a.m.