output/script/self-assembly_isolate.R

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

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

# Augument passed from command line
args = commandArgs(trailingOnly=TRUE)
treatment_name = args[1]

# Make regional species pool
parameter_load(parameter_text = paste0("parameter_script/", treatment_name, ".txt"))
pool_build(save_data = TRUE, data_name = "species_pool.Rdata")

# Make resource environment
resource <- setNames(c(1, rep(0, P-1)), paste0("R", sprintf("%03d", 1:P)))
assign("Rin", c(Rin1, rep(0, times = P-1)), envir = .GlobalEnv) # Supply for each resource. Set to 0

# Modify the `w` and `stoi` of fermenters.
w[1,1:(S_pool/function_group)] <- w_fermenter_P1
stoi[2,1,1:(S_pool/function_group)] <- stoi_fermenter_P1_P2

# Isolates ID
result_merged <- result_read(dir = "simulation_result/", pattern = treatment_name, threshold = threshold)
isolate_vector <- result_merged %>% filter(time == max(time), type == "X") %>% pull(variable) %>% unique() %>% sort()

# Run
for (i in 1:length(isolate_vector)) {
  result <- CR_model(c(resource, setNames(I, isolate_vector[i])),
                     time_limit = time_limit, time_step = 1)
  # Write result file to txt
  parameter_write(result = result, 
                  parameter_list = parameter_list, 
                  file_name = paste0("simulation_result/isolates/", treatment_name, "_", isolate_vector[i], ".txt"))
  print (i)
}