output/script/motif_null.R

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

library(micro.crm)
library(tidyverse)
library(data.table)
library(igraph)

# Augument passed from command line
args = commandArgs(trailingOnly=TRUE)
n = as.numeric(args[1]) # number of node; number of species; richness
b = as.numeric(args[2]) # number of simulations
  
frac <- seq(0, 1, by = .1)

df_list <- rep(list(as.data.frame(matrix(NA, b, 8)) %>% setNames(c(paste0("motif", 1:7), "fracCoext"))), length(frac))

for (i in 1:length(frac)){
  df_list[[i]][,8] <- frac[i]
  for(j in 1:b) {
    df_list[[i]][j,1:7] <- motif_count(null_network_make(n = n, frac_of_coext = frac[i]))
  }
  print(frac[i])
}

# 
do.call("rbind", df_list) %>%
  gather("motif", "count", 1:7) %>%
  write.table(file = paste0("simulation_result/motif_null_n", n, "_", b,".txt"), row.names = F)