R/DAISIE_sim_min_type2.R

In xieshu95/Trait_dependent_TraiSIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

DAISIE_sim_min_type2 = function(time,M,pars,replicates, prop_type2_pool)
{
  island_replicates = list()

  n_islands_with_type2 = 0
  counter = 0
  while(n_islands_with_type2 < replicates)
  {
    pool2 = DDD::roundn(M * prop_type2_pool)
    pool1 = M - pool2
    
    lac_1 = pars[1]
    mu_1 = pars[2]
    K_1 = pars[3]
    gam_1 = pars[4]
    laa_1 = pars[5]
    
    lac_2 = pars[6]
    mu_2 = pars[7]
    K_2 = pars[8]
    gam_2 = pars[9]
    laa_2 = pars[10]
      
    full_list = list()
    
    #### species of pool1
    for (m_spec in 1:pool1)
    { 	
      full_list[[m_spec]] = DAISIE_sim_core(time = time,mainland_n = 1,pars = c(lac_1,mu_1,K_1,gam_1,laa_1))
      full_list[[m_spec]]$type1or2 = 1
    }
    
    #### species of pool2
    for (m_spec in (pool1 + 1):(pool1 + pool2))
    { 	
      full_list[[m_spec]] = DAISIE_sim_core(time = time,mainland_n = 1,pars = c(lac_2,mu_2,K_2,gam_2,laa_2))
      full_list[[m_spec]]$type1or2 = 2
    }
      
    type_2s = which(unlist(full_list)[which(names(unlist(full_list)) == "type1or2")] == 2)
    
    number_type2_species_colonized = 0
    for (i in 1:length(type_2s))
    {
      the_row = full_list[[type_2s[i]]]$stt_table[nrow(full_list[[type_2s[i]]]$stt_table),]
      if(sum(the_row) > 0)
      {
        number_type2_species_colonized = number_type2_species_colonized + 1
      }
    }
      
    if(number_type2_species_colonized > 0)
    {
      n_islands_with_type2 = n_islands_with_type2 + 1
      island_replicates[[length(island_replicates) + 1]] = list() 
      island_replicates[[length(island_replicates)]] = full_list
      print(paste("Number of island replicates with type 2 species: ", length(island_replicates),sep = ""))  
    }
    
    counter = counter + 1
    print(paste("Island ",counter,sep = ""))  
  }
  return(island_replicates)
}