simulate_graph: Simulate species occupancy in one dynamic landscape
In MetaLandSim: Landscape and Range Expansion Simulation

simulate_graph

R Documentation

Simulate species occupancy in one dynamic landscape

Description

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(s)

Frederico Mestre and Fernando Canovas

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
			)

MetaLandSim documentation built on Jan. 13, 2023, 1:11 a.m.