R/manage_landscape_sim.R

In MetaLandSim: Landscape and Range Expansion Simulation

manage_landscape_sim <-
  function(par_df,parameters_spom,full.output = FALSE)
  {
    
    output <- data.frame(matrix(nrow=nrow(par_df),ncol=5))
    colnames(output) <- c("mean occupation","mean number of patches","mean turnover",
                          "mean distance","mean area")
    lines_df <- nrow(par_df)
    for(i in 1:nrow(par_df))
    {
      
      it <- iterate.graph(iter=par_df[i,7],
                          mapsize=par_df[i,5],
                          dist_m=par_df[i,1],
                          areaM=par_df[i,3],
                          areaSD=par_df[i,4],
                          Npatch=par_df[i,2],
                          disp=par_df[i,26],
                          span=par_df[i,6],
                          par1=as.vector(par_df[i,8]),
                          par2=as.vector(par_df[i,9]),
                          par3=as.vector(par_df[i,10]),
                          par4=as.vector(par_df[i,11]),
                          par5=as.vector(par_df[i,12]),
                          method=as.vector(par_df[i,15]),
                          parm=par_df[i,14],
                          nsew=as.vector(par_df[i,13]),
                          succ = as.vector(par_df[i,27]),
                          param_df=parameters_spom,
                          kern=as.vector(par_df[i,16]),
                          conn=as.vector(par_df[i,17]),
                          colnz=as.vector(par_df[i,18]),
                          ext=as.vector(par_df[i,19]),
                          beta1=as.vector(par_df[i,20]),
                          b=par_df[i,21],
                          c1=as.vector(par_df[i,22]),
                          c2=as.vector(par_df[i,23]),
                          z=as.vector(par_df[i,24]),
                          R=as.vector(par_df[i,25]),
                          graph=FALSE)
      
      output[i,1] <- mean(it$occupancy[,"mean"])
      output[i,2] <- mean(it$number_patches[,"mean"])
      output[i,3] <- mean(it$turnover[,"mean"])
      output[i,4] <- mean(it$mean_distance[,"mean"])
      output[i,5] <- mean(it$mean_area[,"mean"])
      
      cat("Completed simulation",i," of ",lines_df,"\n")
      
      if(full.output == TRUE){
        dir.create(file.path(getwd(), 'output'), showWarnings = FALSE)
        save(it, file = paste('output/','simulation_',i,'.RData', sep=''))
        message("Saved simulation",i," in the output folder.","\n")
      }
    }
    
    output2 <- cbind(par_df,output)
    return(output2)
  }