assembly: Simulate Community Assembly

#' #' @title Create random pool of connected species
#' #'
#' #' @param web adjacency matrix.
#' #' @param S number of species.
#' #' @param verbose TRUE/FALSE.
#' #' @param max_iter maximum number of iterations.
#' #' @param plot TRUE/FALSE if to plot the community.
#' #'
#' #' @examples
#' #' a <- connected_pool(web, 13, verbose = FALSE)
#' #' g <- graph_from_adjacency_matrix(web[a, a], "undirected")
#' #' while (igraph::components(g, "strong")$no > 1) {
#' #'   message("Not strongly connected - rerunning")
#' #'   a <- connected_pool(web, 13, verbose = FALSE)
#' #'   g <- graph_from_adjacency_matrix(web[a, a], "undirected")
#' #' }
#' #' plot(g)
#' #' g <- graph_from_adjacency_matrix(web[a, a], "directed")
#' #' all(as.numeric(names(as.numeric(names((degree(g, mode = "in") == 0))))) %in% basal)
#' connected_pool <- function(
#'   web,
#'   S,
#'   verbose = FALSE,
#'   max_iter = 1000,
#'   plot = TRUE,
#'   iter = 0 #do not modify this
#' ) {
#'   pool <- rep(NA, S)
#'   basal <- as.vector(which(colSums(web) == 0)) # get basal species
#'   diff <- S - sum(!is.na(pool))
#'   i <- 0 #counter for while loop exit condition
#'   while (diff != 0 & i < 100) {
#'     # if (verbose) {
#'     #   if (i %% 10 == 0) {
#'     #     message("Missing ", diff, " species")
#'     #   }
#'     # }
#'     available <- setdiff(seq_len(nrow(web)), pool) #get available species
#'     sp <- sample(available, diff) #get random species
#'     basal_present <- intersect(basal, union(pool, sp))
#'     if (length(basal_present) == 0) {
#'       i <- i + 1
#'       next
#'     }
#'     pool <- replace_species(pool, basal_present)
#'     # remove species that have not connected to present basal species
#'     has_resource <- colSums(web[basal_present, union(pool, sp), drop = FALSE]) > 0
#'     no_resource <- which(!has_resource)
#'     no_resource <- setdiff(no_resource, basal)
#'     sp <- setdiff(sp, no_resource)
#'     if (length(sp) == 0) {
#'       i <- i + 1
#'       next
#'     }
#'     pool <- replace_species(pool, sp)
#'     pool <- sort(unique(pool))
#'     isolated <- which(colSums(web[pool, pool, drop = FALSE]) == 0)
#'     isolated <- setdiff(pool[isolated], basal)
#'     pool[which(pool %in% isolated)] <- NA
#'     diff <- S - sum(!is.na(pool))
#'     i <- i + 1
#'   }
#'   if (!check_all_species_have_resources(pool, web)) {
#'     if (iter < max_iter) {
#'       if (verbose) {
#'         message("Unconnected species detected - starting another iteration")
#'       }
#'       pool <- connected_pool(web, S, verbose, max_iter, iter = iter + 1)
#'     } else {
#'       pool <- NULL
#'       warning("Unconnected species detected")
#'     }
#'   } else {
#'     if (verbose) {
#'       message("Connected species pool found")
#'     }
#'     if (plot) {
#'       plot(graph_from_adjacency_matrix(web[pool, pool]))
#'     }
#'     return(pool)
#'   }
#' }
#'
#' #' @title Replace species
#' #' @param species_list vector of species with some NAs to be replaced.
#' #' @param replacements candidates for replacement.
#' #' @return the original vector \code{species_list} with replaced species.
#' replace_species <- function(
#'   species_list,
#'   replacements
#' ) {
#'   replacements <- replacements[!replacements %in% species_list]
#'   to_replace <- which(is.na(species_list))
#'   if (length(replacements) < length(to_replace)) {
#'     to_replace <- to_replace[seq_len(length(replacements))]
#'   } else if (length(replacements) > length(to_replace)) {
#'     replacements <- sample(replacements, length(to_replace))
#'   }
#'   species_list[to_replace] <- replacements
#'   return(species_list)
#' }
#'
#' #' @param pool species list of the local community.
#' #' @param web the metaweb.
#' #' @return TRUE/FALSE
#' check_all_species_have_resources <- function(
#'   pool,
#'   web,
#'   verbose = FALSE
#' ) {
#'   basal_species <- which(colSums(web) == 0)
#'   if (!all(which(colSums(web[pool, pool, drop = FALSE]) == 0) %in% basal_species)) {
#'     if (verbose) {
#'       message("Unconnected species detected")
#'     }
#'     return(FALSE)
#'   } else {
#'     if (verbose) {
#'       message("All species connected")
#'     }
#'     return(TRUE)
#'   }
#' }