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Simulate species occupancy in one dynamic landscape

simulate_graph.Rd

Simulates the species' occupation on a landscape sequence, resorting to the spom function.

Usage

simulate_graph(rl, rlist, simulate.start, method, parm, nsew="none", succ="none", 
param_df, kern, conn, colnz, ext, beta1, b, c1, c2, z, R)

Arguments

rl

Object of class 'landscape' or 'metapopulation'.

rlist

List delivered by span.graph.

simulate.start

TRUE (rl is of class 'landscape') or FALSE (rl is of class 'metapopulation')

method

One of the following: click - individually select the patches with occurrence of the species by clicking on the map. Use only for individual landscape simulations. However, this option should not be used with iterate.graph. percentage - percentage of the patches to by occupied by the species. number - number of patches to be occupied by the species. To be internally passed to species.graph.

parm

Parameter to specify the species occurrence - either percentage of occupied patches or number of occupied patches, depending on the method chosen. To be internally passed to species.graph.

nsew

'N', 'S', 'E', 'W' or none - point of entry of the species in the landscape. By default set to "none". To be internally passed to species.graph.

succ

Set the preference of the species for patch successional stage: 'none', 'early', 'mid' and 'late'.

param_df

Parameter data frame delivered by parameter.estimate, including:

  • alpha - Parameter relating extinction with distance.

  • y - Parameter y in the colonization probability.

  • e - Parameter defining the extinction probability in a patch of unit area.

  • x - Parameter scaling extinction risk with patch area.

To be internally passed to simulate_graph.

kern

'op1' or 'op2'. Dispersal kernel. See details in the spom function. To be internally passed to spom.

conn

'op1' or 'op2'. Connectivity function. See details in the spom function. To be internally passed to spom.

colnz

'op1', 'op2' or 'op3'. Colonization function. See details in the spom function. To be internally passed to spom.

ext

'op1', 'op2' or 'op3'. Extinction function. See details in the spom function. To be internally passed to spom.

beta1

Parameter afecting long distance dispersal probability (if the Kern='op2'). To be internally passed to spom.

b

Parameter scaling emigration with patch area (if conn='op1' or 'op2'). To be internally passed to spom.

c1

Parameter scaling immigration with the focal patch area (if conn='op2'). To be internally passed to spom.

c2

Parameter c in the option 3 of the colonization probability (if colnz='op3'). To be internally passed to spom.

z

Parameter giving the strength of the Allee effect (if colnz='op3'). To be internally passed to spom.

R

Parameter giving the strength of the Rescue effect (if ext='op3'). To be internally passed to spom.

Value

Returns a list of occupied landscapes, representing the same occupied landscape at different time steps.

Author

Frederico Mestre and Fernando Canovas

See also

spom, span.graph, rland.graph, iterate.graph

Examples


data(rland)
data(landscape_change)
data(param1)

sim1 <- simulate_graph(rl=rland, 
      rlist=landscape_change, 
      simulate.start=TRUE, 
      method="percentage", 
      parm=50, 
      nsew="none",
      succ = "none", 
      param_df=param1, 
      kern="op1", 
      conn="op1", 
      colnz="op1", 
      ext="op1", 
      beta1=NULL, 
      b=1, 
      c1=NULL, 
      c2=NULL, 
      z=NULL, 
      R=NULL
      )