R/list.stats.R

In MetaLandSim: Landscape and Range Expansion Simulation

list.stats <-
  function (sim_list, stat, plotG=FALSE)
  {
    sim_list1 <- sim_list[[1]]
    n <- length(sim_list1)
    stat.list <- as.list(rep("", n))
    if(stat == "mean_area")
    {
      for(i in 1:n)
      {
        df_nodes <- sim_list1[[i]]
        if(nrow(df_nodes)==0) mean_area <- 0
        if(nrow(df_nodes)!=0) mean_area <- as.numeric(mean(df_nodes[, "areas"]))
        stat.list[[i]] <- mean_area
      }
    }
    if(stat == "sd_area")
    {
      for(i in 1:n)
      {
        df_nodes <- sim_list1[[i]]
        sd_area <- as.numeric(sd(df_nodes[, "areas"]))
        if(nrow(df_nodes)!=1)stat.list[[i]] <- sd_area
        if(nrow(df_nodes)==1)stat.list[[i]] <- 0
        if(nrow(df_nodes)==0)stat.list[[i]] <- 0
        
      }
    }
    if(stat == "mean_distance")
    {
      for(i in 1:n)
      {
        df_nodes <- sim_list1[[i]]
        if(nrow(df_nodes)!=0){
        xy <- df_nodes[,1:2]
        xy_dist <- pairdist(as.matrix(xy))
        radiuses <- df_nodes$radius
        for(j in 1:nrow(xy_dist))
        {
          xy_dist[,j] <- xy_dist[,j] - radiuses[j]
          xy_dist[j,] <- xy_dist[j,] - radiuses[j]
        }
        xy_dist <- replace(xy_dist, xy_dist<0, 0)
        xy_dist2 <- xy_dist[upper.tri(xy_dist)]
        mean_distance <- mean(xy_dist2)
        if(nrow(xy)!=1)stat.list[[i]] <- mean_distance
        }
        if(nrow(df_nodes)==1)stat.list[[i]] <- 0
        if(nrow(df_nodes)==0)stat.list[[i]] <- 0
      }
    }
    if(stat == "n_patches")
    {
      for(i in 1:n)
      {
        if(nrow(sim_list1[[i]])==0) stat.list[[i]] <- 0
        if(nrow(sim_list1[[i]])!=0) stat.list[[i]] <- nrow(sim_list1[[i]])
      }
    }
    if(stat == "occupation")
    {
      for(i in 1:n)
      {
        df_nodes <- sim_list1[[i]]
        
        if(nrow(sim_list1[[i]])!=0) stat.list[[i]] <- ((sum(sim_list1[[i]]$species)*100)/nrow(sim_list1[[i]]))
        if(nrow(sim_list1[[i]])==0) stat.list[[i]] <- 0
      }
    }
    if(stat == "turnover")
    {
      stat.list <- as.vector(sim_list[[2]])
    }
    if(stat == "mean_nneigh")
    {
      for(i in 1:n){
        df_nodes <- sim_list1[[i]]
        if(nrow(df_nodes)!=0)stat.list[[i]] <- mean(df_nodes$nneighbour)
        if(nrow(df_nodes)==0)stat.list[[i]] <- 0
        
      }
      
      
    }
    stat.list2 <- as.numeric(stat.list)
    if (plotG == TRUE)
    {
      plot(stat.list2, type="l", col="darkgreen", xlab="time", ylab=stat)
    }
    return(stat.list2)
  }