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MetaLandSim is an R package I’ve developed to simulate metapopulational dynamics on an habitat network. It also computes a lot of landscape connectivity metrics and simulates range expansion (check the manual if you are interested).

I’ve mentioned it here frequently, and sometimes I like to post a simple script that I used to answer a user’s question, or a that I’ve written for any other reason. This is a run through the main functions of the package.

Much more complex uses are possible, and I’ve already published a paper with some advanced uses of the package (with another one on the way – I hope!).

Let’s start!

First of all, as always, we should load the package:

# load the package
library(MetaLandSim)
## Warning: package 'MetaLandSim' was built under R version 3.5.1
## Warning: package 'igraph' was built under R version 3.5.1
## ## Attaching package: 'igraph'
## The following objects are masked from 'package:stats':
##
##     decompose, spectrum
## The following object is masked from 'package:base':
##
##     union

Now, to create a random landscape of 10 patches with mean area of 0.2 hectares, and with the landscape mosaic being a square with 1000 meters side.

The species mean dispersal ability is 120 meters (this is merely for graphical purposes, in order to connect the patches producing the graph).

A plot with the landscape graph is displayed graphically.

So… let’s create the landscape:

# set up the plotting window
plot.new()
par(mfrow = c(1,2))

set.seed(200)
rl1 <- rland.graph(mapsize = 1000,
dist_m = 80,
areaM = 0.2,
areaSD = 0.115,
Npatch = 10,
disp = 120,
plotG = TRUE)

# look at the node.characteristics
nodes <- rl1$nodes.characteristics nodes And this data frame shows the characteristics of each patch: ## x y areas radius cluster colour nneighbour ID ## 1 533.7724 583.76503 0.18420882 24.214766 1 #FF0000FF 102.9282 1 ## 2 454.3649 649.25291 0.10651184 18.412977 1 #FF0000FF 102.9282 2 ## 3 589.5783 691.03989 0.04015217 11.305234 2 #FFBF00FF 120.9222 3 ## 4 667.3315 839.29374 0.08311528 16.265428 3 #80FF00FF 167.4060 4 ## 5 711.6001 96.50122 0.36824823 34.236976 4 #00FF40FF 149.0693 5 ## 6 523.8247 235.35054 0.12806475 20.190165 5 #00FFFFFF 112.1129 6 ## 7 566.7674 131.78785 0.01301267 6.435886 5 #00FFFFFF 112.1129 7 ## 8 153.7271 649.28867 0.28659388 30.203587 6 #0040FFFF 300.6378 8 ## 9 383.2137 307.29806 0.15232900 22.019951 7 #8000FFFF 157.9491 9 ## 10 922.1776 646.32962 0.20853287 25.763943 8 #FF00BFFF 319.6587 10 # label the node points text(x = nodes[,'x'],y = nodes[,'y'], pos = 2, offset = .5, labels = as.character(nodes[,'ID'])) # look at information associated with this object # note the class is a landscape class(rl1) ## [1] "landscape" names(rl1) ## [1] "mapsize" "minimum.distance" "mean.area" ## [4] "SD.area" "number.patches" "dispersal" ## [7] "nodes.characteristics" In order to look at the structure of the object ‘rl1’, our random landscape (the graph): str(rl1) ## List of 7 ##$ mapsize              : num 1000
##  $minimum.distance : num 80 ##$ mean.area            : num 0.157
##  $SD.area : num 0.11 ##$ number.patches       : int 10
##  $dispersal : num 120 ##$ nodes.characteristics:'data.frame':   10 obs. of  8 variables:
##   ..$x : num [1:10] 534 454 590 667 712 ... ## ..$ y         : num [1:10] 583.8 649.3 691 839.3 96.5 ...
##   ..$areas : num [1:10] 0.1842 0.1065 0.0402 0.0831 0.3682 ... ## ..$ radius    : num [1:10] 24.2 18.4 11.3 16.3 34.2 ...
##   ..$cluster : int [1:10] 1 1 2 3 4 5 5 6 7 8 ## ..$ colour    : Factor w/ 8 levels "#0040FFFF","#00FF40FF",..: 6 6 8 5 2 3 3 1 4 7
##   ..$nneighbour: num [1:10] 103 103 121 167 149 ... ## ..$ ID        : int [1:10] 1 2 3 4 5 6 7 8 9 10
##  - attr(*, "class")= chr "landscape"

Obtaining the summary of the landscape:

summary_landscape(rl1)
##                                             Value
## landscape area (hectares)                 100.000
## number of patches                          10.000
## mean patch area (hectares)                  0.157
## SD patch area                               0.110
## mean distance amongst patches (meters)    391.228
## minimum distance amongst patches (meters)  60.300

This landscape is really a mathematical graph, where edges connect nodes (points) if they are within the dispersal distance:

help('edge.graph')
e1 <- edge.graph(rl1)
e1
##   ID node A node B   area ndA  area ndB       XA       YA       XB
## 1  1      2      1 0.10651184 0.1842088 454.3649 649.2529 533.7724
## 2  2      7      6 0.01301267 0.1280648 566.7674 131.7879 523.8247
##         YB distance
## 1 583.7650 102.9282
## 2 235.3505 112.1129

And now, let’s populate the patches with a species, considering that red is empty, green is occupied:

help('species.graph')
set.seed(10)
sp_t0 <- species.graph(rl = rl1,
method = "percentage",
parm = 50,
nsew = "none",
plotG = TRUE)

# label the node points
text(x = nodes[,'x'],y = nodes[,'y'], pos = 2, offset = 0.5, labels = as.character(nodes[,'ID']))

This figure shows the empty landscape on the left (rl1) and the occupied on the right (sp_t0):

Look at the information regarding this object. Note the class is metapopulation also note the addition of element ‘distance.to.neighbors’.

Let’s check the class of object ‘sp_t0’:

class(sp_t0)
## [1] "metapopulation"
names(sp_t0)
## [1] "mapsize"                "minimum.distance"
## [3] "mean.area"              "SD.area"
## [5] "number.patches"         "dispersal"
## [7] "distance.to.neighbours" "nodes.characteristics"

And now, looking at the structure of ‘sp_t0’:

str(sp_t0)
## List of 8
##  $mapsize : num 1000 ##$ minimum.distance      : num 80
##  $mean.area : num 0.157 ##$ SD.area               : num 0.11
##  $number.patches : num 10 ##$ dispersal             : num 120
##  $distance.to.neighbours:'data.frame': 10 obs. of 10 variables: ## ..$ 1 : num [1:10] 0 103 121 288 519 ...
##   ..$2 : num [1:10] 103 0 142 285 610 ... ## ..$ 3 : num [1:10] 121 142 0 167 607 ...
##   ..$4 : num [1:10] 288 285 167 0 744 ... ## ..$ 5 : num [1:10] 519 610 607 744 0 ...
##   ..$6 : num [1:10] 349 420 460 621 234 ... ## ..$ 7 : num [1:10] 453 530 560 715 149 ...
##   ..$8 : num [1:10] 386 301 438 548 785 ... ## ..$ 9 : num [1:10] 315 349 436 603 390 ...
##   ..$10: num [1:10] 393 468 336 320 589 ... ##$ nodes.characteristics :'data.frame':  10 obs. of  9 variables:
##   ..$x : num [1:10] 534 454 590 667 712 ... ## ..$ y         : num [1:10] 583.8 649.3 691 839.3 96.5 ...
##   ..$areas : num [1:10] 0.1842 0.1065 0.0402 0.0831 0.3682 ... ## ..$ radius    : num [1:10] 24.2 18.4 11.3 16.3 34.2 ...
##   ..$cluster : int [1:10] 1 1 2 3 4 5 5 6 7 8 ## ..$ colour    : Factor w/ 8 levels "#0040FFFF","#00FF40FF",..: 6 6 8 5 2 3 3 1 4 7
##   ..$nneighbour: num [1:10] 103 103 121 167 149 ... ## ..$ ID        : int [1:10] 1 2 3 4 5 6 7 8 9 10
##   ..$species : num [1:10] 1 0 1 1 1 1 0 0 0 0 ## - attr(*, "class")= chr "metapopulation" Look at some elements like distance.to.neighbors: head(sp_t0$distance.to.neighbours, n = 3)
##          1        2        3        4        5        6        7        8
## 1   0.0000 102.9282 120.9222 288.3278 518.6990 348.5565 453.1799 385.6524
## 2 102.9282   0.0000 141.5232 285.4300 609.6756 419.6902 529.5323 300.6378
## 3 120.9222 141.5232   0.0000 167.4060 606.9312 460.4089 559.7171 437.8463
##          9       10
## 1 314.8046 393.4118
## 2 349.2787 467.8218
## 3 435.7111 335.5909

Note the species column in nodes.characteristics, it contains the information on the presence and absence of the focal species in the habitat network:

sp_t0$nodes.characteristics ## x y areas radius cluster colour nneighbour ID ## 1 533.7724 583.76503 0.18420882 24.214766 1 #FF0000FF 102.9282 1 ## 2 454.3649 649.25291 0.10651184 18.412977 1 #FF0000FF 102.9282 2 ## 3 589.5783 691.03989 0.04015217 11.305234 2 #FFBF00FF 120.9222 3 ## 4 667.3315 839.29374 0.08311528 16.265428 3 #80FF00FF 167.4060 4 ## 5 711.6001 96.50122 0.36824823 34.236976 4 #00FF40FF 149.0693 5 ## 6 523.8247 235.35054 0.12806475 20.190165 5 #00FFFFFF 112.1129 6 ## 7 566.7674 131.78785 0.01301267 6.435886 5 #00FFFFFF 112.1129 7 ## 8 153.7271 649.28867 0.28659388 30.203587 6 #0040FFFF 300.6378 8 ## 9 383.2137 307.29806 0.15232900 22.019951 7 #8000FFFF 157.9491 9 ## 10 922.1776 646.32962 0.20853287 25.763943 8 #FF00BFFF 319.6587 10 ## species ## 1 1 ## 2 0 ## 3 1 ## 4 1 ## 5 1 ## 6 1 ## 7 0 ## 8 0 ## 9 0 ## 10 0 Summarizing the object ‘sp_t0’: summary_metapopulation(sp_t0) ## Value ## landscape area (hectares) 100.000 ## number of patches 10.000 ## mean patch area (hectares) 0.157 ## SD patch area 0.110 ## mean distance amongst patches (meters) 391.228 ## minimum distance amongst patches (meters) 60.300 ## species occurrence - snapshot 1 50.000 And now, finally, we can simulate the occupation on the next time step (function ”spom’), after defining the parameters setting up the options for the simulation: # ultimately we need to provide the 'rules' by which patch dynamics occur; notice there several options help("spom") # establish parameters that control changes in occupancy through time; here use the built-in dataset that contains the key parameters help('param1') data(param1) # view this object; note the four parameters named alpha, x, y, e; these will be used to control our dynamics View(param1) # to simulate dynamics through time, use spom function # spom stands for stochastic patch occupancy model help('spom') sp_t1 <- spom(sp_t0, kern = "op1", conn = "op1", colnz = "op1", ext = "op1", param_df = param1, beta1 = NULL, b = 1, c1 = NULL, c2 = NULL, z = NULL, R = NULL) class(sp_t1) ## [1] "list" The dynamics are contained in the data frame ‘nodes.characteristic’. It depicts the species presence at time step t (species), time step t+1 (species2) and turnover: head(sp_t1$nodes.characteristics)
##          x         y      areas   radius cluster    colour nneighbour ID
## 1 533.7724 583.76503 0.18420882 24.21477       1 #FF0000FF   102.9282  1
## 2 454.3649 649.25291 0.10651184 18.41298       1 #FF0000FF   102.9282  2
## 3 589.5783 691.03989 0.04015217 11.30523       2 #FFBF00FF   120.9222  3
## 4 667.3315 839.29374 0.08311528 16.26543       3 #80FF00FF   167.4060  4
## 5 711.6001  96.50122 0.36824823 34.23698       4 #00FF40FF   149.0693  5
## 6 523.8247 235.35054 0.12806475 20.19017       5 #00FFFFFF   112.1129  6
##   species species2 turn
## 1       1        1    0
## 2       0        0    0
## 3       1        1    0
## 4       1        1    0
## 5       1        1    0
## 6       1        1    0

To simulate the dynamics across multiple steps and get the results use the ‘iterate.graph’ function, which runs the full simulation:

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)
## Completed iteration 1  of  2
## Completed iteration 2  of  2

Which will open the web browser with the following graphs:

And that’s all for now!

Thanks!

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