metacommunity | R Documentation |
Functions to generate a metacommunity
object.
metacommunity(partition, similarity) ## S4 method for signature 'data.frame,missing' metacommunity(partition) ## S4 method for signature 'numeric,missing' metacommunity(partition) ## S4 method for signature 'matrix,missing' metacommunity(partition) ## S4 method for signature 'missing,similarity' metacommunity(partition, similarity) ## S4 method for signature 'numeric,similarity' metacommunity(partition, similarity) ## S4 method for signature 'data.frame,similarity' metacommunity(partition, similarity) ## S4 method for signature 'matrix,similarity' metacommunity(partition, similarity)
partition |
two-dimensional |
similarity |
(optional) object of class |
metacommunity()
returns an object of class
metacommunity
(see 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 pairwise
similarities between 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
denoting the type of diversity
being calculated. This can be "naive", "genetic", "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
metacommunity-class
# Naive-type partition <- cbind(a = c(1,1,1,0,0), b = c(0,1,0,1,1)) row.names(partition) <- paste0("sp", 1:5) partition <- partition / sum(partition) meta <- metacommunity(partition)
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