Simulate landscape series occupation

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", 
    succ="none", 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/decrease of the mean area of patches, without changing SD.
'stoc' simultaneous creation and destruction of patches.
'ncsd' simultaneous creation and destruction of patches to the north and south of the landscape.
'aggr' correlated habitat destruction.
'none' no change.

To be internally passed to span.graph.

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 par1 = 'stoc'); 'northerndness' of created patches (if par1 = 'ncsd'); percentage of destroyed patches (if par1 = 'aggr'). To be internally passed to span.graph. Default NULL.

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, in hectares (if par1='darea'). To be internally passed to span.graph. Default NULL.

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 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 affecting 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. By default set to 1.

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.

graph

TRUE/FALSE, to show graphic output.

Value

Returns a list of five data frames with information regarding the values of mean area, mean inter-patch distance, number of patches occupancy and patch occupancy turnover in each of the iterations, as well as the mean values and SD.

References

References in the spom function.

Author

Frederico Mestre and Fernando Canovas

Examples

if (FALSE) { # \dontrun{
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 = NULL, par4 = NULL, 
      par5 = NULL, 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, graph =TRUE)
} # }