R/matrix.graph.R

In MetaLandSim: Landscape and Range Expansion Simulation

matrix.graph <-
function(rl,mat)
  {
    
  if(!inherits(rl, "landscape"))
  #if(class(rl) != "landscape") 
        {
          stop(paste(rl, " should be an object of class class 'landscape'.", sep=""), call. = FALSE)
        }
    df1 <- rl$nodes.characteristics
    disp <- rl$dispersal
    if(mat == "euc_distance")
      {
        result <- pairdist(df1[,1:2])
        result <- as.data.frame(result)
        names(result) <- df1$ID
        rownames(result) <- df1$ID
        radiuses <- cbind(df1$ID,df1$radius)
        for(i in 1:nrow(result))
         {
            result[,i] <- result[,i] - radiuses[i,2]
            result[i,] <- result[i,] - radiuses[i,2]
          }
        result <- replace(result, result<0, 0)
        result <- as.matrix(result)
      }
    if(mat == "centr_distance")
      {
        result <- pairdist(df1[,1:2])
        result <- as.data.frame(result)
        names(result) <- df1$ID
        rownames(result) <- df1$ID
        result <- as.matrix(result)
      }
	if(mat == "adjacency")
      {
        df2 <- pairdist(df1[,1:2]) 
        df3 <- df2<disp
        df4 <- df3+0
        diag(df4) <- NA
        result <- as.data.frame(df4)
        names(result) <- df1$ID
        rownames(result) <- df1$ID
        result <- as.matrix(result)
      }
    if(mat == "top_matrix")
      {
        df1 <- rl$nodes.characteristics
        disp <- rl$dispersal
        m <- df1[,c(8,1,2)]
        m2 <- as.matrix(m[,2:3])
        m3 <- pairdist(m2)
        m3[m3>disp] <- 0
        m3[m3 == 0] <- NA
        m4 <- allShortestPaths(m3)
        nnodes <- ncol(m3)
        m5 <- matrix(NA,nnodes,nnodes)
        for (i in 1:nnodes)
          {
            for (j in 1:nnodes)
              {
                a <- extractPath(m4, i, j)
                m5[i,j] <- length(a)-1
              }
          }
        m5[m5 == 1] <- 0
        m3[m3 > 0] <- 1
        m3[is.na(m3)] <- 0
        m6 <- m5+m3
		m6[lower.tri(m6)] <- NA
        diag(m6) <- 0
        result <- as.data.frame(m6)
        names(result) <- df1$ID
        rownames(result) <- df1$ID
        result <- as.matrix(result)
      }
 	return(result)
  }