R/network_make.R

In Chang-Yu-Chang/MigrationCommunity: Microbial Consumer-Resource Model

#' Make network
#' @description Make network for a competitive network from nodes and edges
#' @name network_make
#' @param nodes node list
#' @param edges edge list
#' @return an `igraph` object

network_make <- function(nodes, edges) {

  # Nodes and edges
  nodes <- filter(nodes)
  edges <- filter(edges) %>% dplyr::select(from, to, interaction)

  # Make undirected edges for coexistence pairs
  edges_coext <- filter(edges, interaction == "coexistence")
  edges_coext[, c("from", "to")] <- edges_coext[, c("to", "from")]
  edges <- rbind(edges, edges_coext) # Edges for coexistence links

  # Make undirected edges for non-growth pairs
  edges_nongrowth <- filter(edges, interaction == "non-growth")
  edges_nongrowth[, c("from", "to")] <- edges_nongrowth[, c("to", "from")]
  edges <- rbind(edges, edges_nongrowth) # Edges for coexistence links


  # Make graph
  net <- graph_from_data_frame(d = edges, vertices = nodes, directed = T)

  # Edges attributes
  edge_colrs <- c("blue", "red", "grey90")
  E(net)$arrow.size <- .2
  E(net)$edge.color[E(net)$interaction == "exclusion"] <- 1
  E(net)$edge.color[E(net)$interaction == "coexistence"] <- 2
  E(net)$edge.color[E(net)$interaction == "non-growth"] <- 3

  return(net)
}