iterate.graph: Simulate landscape series occupation

Description

Repeats the process of simulation by simulate_graph as many times as required (argument 'iter').

Usage

iterate.graph(iter, mapsize, dist_m, areaM, areaSD, Npatch, disp, 
		span, par1 = 'none', par2 = NULL, par3 = NULL, par4 = NULL, 
		par5 = NULL, method = 'percentage', parm, nsew = 'none', 
		a_min, param_df, kern, conn, colnz, ext, beta1, 
		b = 1, c1 = NULL, c2 = NULL, z = NULL, R = NULL, graph)

Arguments

iter

Number of repetitions of the simulation.

mapsize

Landscape mosaic side length, in meters. To be internally passed to rland.graph.

dist_m

Minimum distance between patches (centroid). To be internally passed to rland.graph.

areaM

Mean area (in hectares). To be internally passed to rland.graph.

areaSD

SD of the area of patches, in order to give variability to the patches area. To be internally passed to rland.graph.

Npatch

Number of patches (might be impaired by the dist_m, see the "Note" section). To be internally passed to rland.graph.

disp

Species mean dispersal ability, in meters. To be internally passed to rland.graph.

span

Number of time steps (e.g. years) to simulate. To be internally passed to span.graph.

par1

One of the following (default 'none'):

'hab' percentage of the number of patches to eliminate.
'dincr' minimal distance (between centroids of patches) increase over the simulation (in meters).
'darea' percentage of increase/decreas

par2

Parameter specifying details for the options in par1: percentage of patches do delete (if par1 = 'hab'); distance, in meters (if par1 = 'dincr'); percentage of increase/decrease of the mean area of patches (if par1 = 'area'); percentage of new patches (if

par3

Additional parameter specifying details for the options in par1: percentage of destroyed patches (if par1 = 'stoc'); 'southerndness' of destroyed patches (if par1 = 'ncsd'); aggregation of destruction (if par1 = 'aggr'). Minimum area for patch deletion, i

par4

Percentage of created patches (if par1 = 'ncsd'). To be internally passed to span.graph. Default NULL.

par5

Percentage of destroyed patches (if par1 = 'ncsd'). To be internally passed to span.graph. Default NULL.

method

One of the following (default 'percentage'): 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 i

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.

a_min

Minimum patch area of the patches to be occupied (in hectares). To be internally passed to species.graph.

param_df

Parameter data frame delivered by parameter.estimate, including:

alpha - Parameter relating extinction with distance.
y - Parameter y in the colonization probability.
e -

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

Parameter scaling emigration with patch area (if conn='op1' or 'op2'). To be internally passed to spom. By default set to 1.

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

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

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

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

graph

TRUE/FALSE, to show graphic output.

Value

Returns a list of data frames with the dispersal probability to the north, south, east and west:
NORTHData frame with the following columns: DISTANCE (computed using mapsize*number of the landscape mosaic), OCCUPATION (number of repetitions this landscape mosaic is occupied) and PROPORTION (proportion of repetitions at which this landscape mosaic is occupied)
SOUTHSame as NORTH.
EASTSame as NORTH.
WESTSame as NORTH.

References

References in the spom function.

Examples

Run this code

data(param1)

#Example with 2 iterations (ideally >100):

it1 <- iterate.graph(iter = 2, mapsize =10000, dist_m = 10, areaM = 0.05, 
			areaSD = 0.02, Npatch = 250, disp = 800, span = 100, 
			par1 = "hab", par2 = 2, par3 = 0.0001, par4 = NULL, 
			par5 = NULL, method = "percentage", parm = 50, 
			nsew = "none", a_min = 0, param_df = param1, 
			kern = "op1", conn = "op1", colnz = "op1", ext = "op1", 
			beta1 = NULL, b = 1, c1 = NULL, c2 = NULL, z = NULL, 
			R = NULL, graph =TRUE)

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