library(tidyverse)
library(deSolve)
library(data.table)
library(micro.crm)
#rm(list= ls())
# Augument passed from command line
args = commandArgs(trailingOnly=TRUE)
treatment_name = args[1]
# Make regional species pool
#treatment_name <- "migration-parent001"
parameter_load(parameter_text = paste0("parameter_script/", treatment_name, ".txt"))
pool_build(save_data = F)
# Make resource environment
resource <- setNames(c(R1_initial, 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
# Run
for (r in 1:replicate) {
result_list <- rep(list(NA), migration_event+1)
comm = NULL
for (i in 1:migration_event) {
# Simulation
result <- community_generate(pool = regional_pool, I = I, threshold = threshold) %>%
community_coalesce(resource, comm / sum(comm) * I) %>% # Consumers and resource from previous transfer
CR_model(time_limit = migration_time_limit, time_step = 1)
# Time
result$time <- result$time + migration_time_limit*(i-1)
# Save result to the main list
result_list[[i]] <- result
# Take the final time step
temp <- filter(result, time == max(time), value >= threshold) %>% dplyr::select(-time)
comm <- setNames(temp$value, temp$variable)
}
# Final time step
result <-
community_generate(pool = regional_pool, I = I, threshold = threshold, seed = r*(migration_event+1)) %>% # Draw from pool
community_coalesce(resource, comm / sum(comm) * I) %>%
CR_model(time_limit = time_limit, time_step = 1) # migration_time_limit or time_limit
# Time
result$time <- result$time + migration_time_limit*migration_event
result_list[[migration_event+1]] <- result
# Merge all migration events
result_merged <- rbindlist(result_list)
# Write result file to txt
parameter_write(result = result_merged,
parameter_list = parameter_list,
file_name = paste0("simulation_result/", treatment_name,"_", sprintf("%03d", r),".txt"))
# Report progress
print(r)
}
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