R_script_in_development/fn.metaSIM.disturbance.R

In sokole/MCSim: Metacommunity simulations for ecologists

#############
# send function landscape list and interval duration list, along with other metaSim parameters that will be fixed across all simulations
fn.metaSIM.disturbance <- function(
  
  scenario_name, # text string
  landscape_list, # list of landscapes to run in series
  time_interval_durations, # vector of integers representing the number of timesteps to use for each landscape in the landscape_list, same length as landscape_list
  ...){

my_scenario_ID <- paste0(scenario_name,'_', Sys.time() %>% format('%Y%m%d_%H%M%S'))
# A data frame with coordinates for 5 sites

sim_result_list <- list()
###################
for (i_ts in 1:length(landscape_list)){
  
  #################
  if(!is.null(names(landscape_list))){
    sim_id_name <- names(landscape_list)[i_ts]
  }else{
    sim_id_name <- paste0('TS',i_ts)
  }
  
  if(i_ts == 1){
    sim_result_list[[i_ts]] <- MCSim::fn.metaSIM(
      landscape = landscape_list[[i_ts]],
      n.timestep = time_interval_durations[i_ts], 
      scenario.ID = my_scenario_ID,
      sim.ID = sim_id_name,
      ...) 
  }else if(i_ts > 1){
    J_last_timestep_long <- sim_result_list[[i_ts - 1]]$J.long %>% 
      filter(timestep == max(timestep)) 
    
    last_time_step_number <- sim_result_list[[i_ts - 1]]$J.long$timestep %>% max()
    
    J_last_timestep_wide <- J_last_timestep_long %>%
      select(site, spp, count) %>%
      group_by(site) %>%
      ungroup() %>%
      spread(spp, count, fill = 0) %>%
      column_to_rownames('site') %>%
      as.data.frame()
    
    sim_result_list[[i_ts]] <- MCSim::fn.metaSIM(
      landscape = landscape_list[[i_ts]],
      J.t0 = J_last_timestep_wide,
      n.timestep = time_interval_durations[i_ts], 
      scenario.ID = my_scenario_ID,
      sim.ID = sim_id_name,
      ...) 
    
    # modify timestep to be global for combined time series
    sim_result_list[[i_ts]]$J.long <- sim_result_list[[i_ts]]$J.long %>% mutate(timestep = timestep + last_time_step_number)
  }
  
  # add simulation info to link output to metadata
  sim_result_list[[i_ts]]$J.long <- sim_result_list[[i_ts]]$J.long %>% mutate(
    scenario.ID = sim_result_list[[i_ts]]$scenario.ID,
    sim.result.name = sim_result_list[[i_ts]]$sim.result.name)
}

return(
  list(
    scenario.ID = sim_result_list[[1]]$scenario.ID,
    sim.result.name.list = sim_result_list %>% purrr::map(`[`, "sim.result.name"),
    landscape.list = landscape_list,
    dat.gamma.t0.list = sim_result_list %>% purrr::map(`[`, "dat.gamma.t0"),
    W.r.list = sim_result_list %>% purrr::map(`[`, "W.r"),
    J.long = sim_result_list %>% purrr::map(`[`, "J.long") %>%
      flatten() %>% bind_rows()
  ))
} #END FUNCTION