metacommunity-class: metacommunity-class

In boydorr/rdiversity: Measurement and Partitioning of Similarity-Sensitive Biodiversity

metacommunity-class

Description

Container for class metacommunity.

Usage

## S4 method for signature 'metacommunity'
show(object)

Arguments

object

object of class metacommunity

Fields

type_abundance

two-dimensional matrix of mode numeric with rows as types (species), columns as subcommunities, and each element containing the relative abundance of types in each subcommunity relative to the metacommunity as a whole. In the phylogenetic case, this corresponds to the proportional abundance of historical species, which is calculated from the proportional abundance of terminal taxa

similarity

two-dimensional matrix of mode numeric with rows as types, columns as types, and elements containing the pairwise similarity of types

similarity_components

list containing the components necessary to calculate similarity. This list is empty when precompute_dist = TRUE when calculating distance. When a pairwise distance matrix is too large and precompute_dist = FALSE, this list contains all the information required to calculate pairwise distance between types

similarity_parameters

list containing parameters associated with converting pairwise distances to similarities (the dist2sim() arguments)

ordinariness

two-dimensional matrix of mode numeric with rows as types, columns as subcommunities, and elements containing the ordinariness of types within subcommunities

subcommunity_weights

vector of mode numeric containing subcommunity weights

type_weights

two-dimensional matrix of mode numeric, with rows as types, columns as subcommunities, and elements containing weights of types within a subcommunity

dat_id

object of class character describing the class of distance / similarity being used, e.g. "naive", "taxonomic", and so on

raw_abundance

[Phylogenetic] two-dimensional matrix of mode numeric with rows as types, columns as subcommunities, and elements containing the relative abundance of present day species

raw_structure

[Phylogenetic] two-dimensional matrix of mode numeric with rows as historical species, columns as present day species, and elements containing historical species lengths within lineages

parameters

[Phylogenetic] data.frame containing parameters associated with each historic species in the phylogeny

boydorr/rdiversity documentation built on May 6, 2022, 10:56 a.m.