[R] Adding a migration element to a deterministic spatial model

[Aimee Jones]

Hi all,
I've been working with a friend's model that is a spatial model
consisting of 4 patches. She uses the code found below to add
migration between the patches for the three species of concern. When I
run a script incorporating this code, all four patches run
independently without migration occuring. When I type m1[1,2] into the
workspace to see if it will return a figure, it returns, error, object
m1 not found. However, if I type the code below directly into the
workspace, it finds and returns m1[1,2] (or any other value). I have
tried to find other examples of code that add a migration element to a
spatial model but have not had any success. I need help figuring out
why m#[i,j] consistently returns a 0 value (or at least appears to)
despite the code instructing R to return different values under set
circumstances.

thanks for any help you are able to give,
yours sincerely,
Aimee


with(as.list(c(y,p)),
 {

  dydt <- rep(0,NP*16)



  # Initialize m1,m2,m3
  m1 <- matrix(0,NP,NP)
  m2 <- matrix(0,NP,NP)
  m3 <- matrix(0,NP,NP)



 	
  # Only nearest neighbors have nonzero travel rates between each other
  for (i in 1:NP)
  {
   for (j in 1:NP)
   {
    if ((i%%sqrt(NP)) == 0 & i!=j)
    {
     if (j == i+sqrt(NP) | j == i-1 | j == i-sqrt(NP))
     {
      m1[j,i] <- 0.1
      m1[i,j] <- 0.1

      m2[j,i] <- 0.25
      m2[i,j] <- 0.25

      m3[j,i] <- 0.1
      m3[i,j] <- 0.1
     }
    }
    if (i%%sqrt(NP) == 1)
    {
     if (j == i+sqrt(NP) | j == i+1 | j == i-sqrt(NP))
     {
      m1[j,i] <- 0.1
      m1[i,j] <- 0.1

      m2[j,i] <- 0.25
      m2[i,j] <- 0.25

      m3[j,i] <- 0.1
      m3[i,j] <- 0.1
     }
    }
				
    if (i%%sqrt(NP)!=0 & i%%sqrt(NP)!=1 & i!=j)
    {
     if (j == i+sqrt(NP) | j == i+1 | j == i-sqrt(NP)| j == i-1)
     {
      m1[j,i] <- 0.1
      m1[i,j] <- 0.1

      m2[j,i] <- 0.25
      m2[i,j] <- 0.25

      m3[j,i] <- 0.1
      m3[i,j] <- 0.1
     }
    }
   }
  }

		
  # Initialize the summaries of incoming movements to a patch
  s <- rep(0,NP*16)

  for (i in 1:NP)
  {
	z <- (i-1)*16

	for (k in 3:6)
	{
		for (j in 1:NP)
		{
			zz <- (j-1)*16
			s[z+k] <- s[z+k] + m1[i,j]*y[zz+k]
		}
	}
	
	for (k in 7:11)
	{
		for (j in 1:NP)
		{
			zz <- (j-1)*16
			s[z+k] <- s[z+k] + m2[i,j]*y[zz+k]
		}
	}

	for (k in 13:16)
	{
		for (j in 1:NP)
		{
			zz <- (j-1)*16
			s[z+k] <- s[z+k] + m3[i,j]*y[zz+k]
		}
	}