freqMat_2_edge: Convert a frequency interaction matrix to an edge list

In txm676/nos: Compute Node Overlap and Segregation in Ecological Networks

Convert a frequency interaction matrix to an edge list

Description

Converts frequency interaction matrices, as used with the bipartite R package, into edge lists. The input matrix can be either a matrix representing a bipartite graph or a squared adjacency matrix. As the functions in the 'nos' R package are based on presence-absence data, all interactions greater than or equal to 1 are set to 1.

Usage

freqMat_2_edge(x, bip = FALSE, sp_nam = FALSE)

Arguments

x	A frequency interaction matrix, in which rows and columns represent species and each value should be numeric, indicating the number of interactions between two species. The input frequency interaction matrix can be in the form of a squared adjacency matrix (e.g. a food web, where the rows and columns represent the same set of species) or representing a bipartite graph where rows and columns correspond to different entities. In regards to the latter, the rows must correspond to species that are consumed (or pollinated etc) and columns are those species that are the consumers (or pollinators etc). For example, for a plant-pollinator interaction matrix, the rows would be the plant species, and the columns the pollinator species. The input interaction matrix can be a dataframe or a matrix. The names of the species can be set as the rownames and column names of the interaction matrix prior to running the function; if names are not provided, the function automatically names the species (see below). As the functions in the 'nos' R package are based on presence-absence data, all interactions greater than or equal to 1 are set to 1. Cannibalistic interactions are allowed, i.e. the same species can be in a row and column.
bip	A logical value describing whether the input matrix represents a bipartite graph (bip = TRUE), or a squared adjaceny matrix (bip = FALSE: the default).
sp_nam	A logical value describing whether the user has provided. species names i.e. row and column names (sp_nam = TRUE) or not (sp_nam = FALSE: the default).If species names are not provided and the input matrix is a squared adjaceny matrix, the rows and columns are given the same identity values (i.e. numbers). If the input matrix represent a bipartite graph, rows and columns are assumed to correspond to different entities and are given different unique values.

Value

An edge list in the form of a dataframe. Each value in a column is a node (e.g. a food item in a trophic-web). Nodes are set as numeric values. For each row (i.e. node pair), the value in the first column is 'consumed' (or pollinated, parasitized etc) by the value in the second column.

Examples

sim_dat <- matrix(c(0, 2, 1, 0, 1, 2, 0, 1), ncol = 4) #simulate bipartite matrix
rownames(sim_dat) <- c("A", "B") #name the consumed species
colnames(sim_dat) <- c("C", "D", "A", "E") #name the consumer species
freqMat_2_edge(sim_dat, bip = TRUE, sp_nam = TRUE)

txm676/nos documentation built on March 28, 2024, 7:44 a.m.