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delta_competition_example.md 4.13 KB
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# A first model of meta population

In this script, we model the evolution of a population where agents are simply defined by their position on some landscape. We implement the simplest possible birth and death function.

## The landscape
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Let's start by a linear landscape. We define a discrete segment of length `9`, with reflecting boundary conditions. In fact, reflecting boundary conditions are implemented for any finite space.

!!! warning "1D Reflections"
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    As of v1, only reflections on one dimensional space are implemented. We have a two dimensional reflection method that will be released in the future.
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There are two ways of implementing a linear landscape. The first one uses a `DiscreteSegment` while the second relies on LightGraphs.jl library. Both are *almost* equivalent.

### DiscreteSegment
```julia
using ABMEv
nodes = 10
mysegment = DiscreteSegment(1,nodes)
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wholespace = (mysegment,)
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```

### grid
```julia
using ABMEv, LightGraphs
nodes = 10
g = grid([nodes,1])
mysegmentgraph = GraphSpace(g)
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wholespace = (mysegmentgraph,)
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```
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!!! warning "Space tuple"
    Notice that the whole space should be a *tuple of spaces*. Even where there is only one sub vector space as here, you need to have brackets and comma around the unit vector space.
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Here is how you can visualise the landscape.

```julia
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using GraphPlot
gplot(g, collect(1:nodes), collect(1:nodes))
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```

## Defining competition processes
We propose that any individual have a constant birth rate, and competes with all the individuals present in the same patch. Let ``i \in \N``,``x_i \in \{1,2,\dots,9\}``.
The competition pressure experience by individual ``i`` is such that

```math
d(x_i) = \sum_j \delta(x_i-x_j)
```
where ``\delta`` is the dirac function.

In this way, we recover a logistic growth function for subpopulation within a patch.

```julia
K0 = 1000 # We will have in total 1000 individuals
b(X,t) = 1 / nodes
d(X,Y,t) = (X[1]  Y[1]) / K0
```
At equilibrium, population size in each deme will reach `K0 / nodes`.

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!!! warning "Time dependency"
    Even though time is not used, you have to write birth and death functions with time dependency.

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## Dispersal
We assume that anytime an offspring is born, it is given a chance to move (`\mu = 1`).
```julia
mu = [1.]
D = (1.5,)
```
## Running the world
We initialise the world with initial population of size ``K_0 / 9`` located on patch `5`. We keep track of individuals' ancestors by setting `ancestors=true`. Because we wish to use `Gillepsie` algorithm, we need `rates=true` as agents' internal birth and death rates are updated at every time step.
!!! note "Warning"
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    `rates` treatment is something we might implement in the library internals.
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```julia
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using UnPack# useful macro @pack!
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NMax = 2000
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tend = 300.
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p = Dict{String,Any}();@pack! p = d,b,D,mu,NMax
myagents = [Agent(myspace,(5,),ancestors=true,rates=true) for i in 1:K0/nodes]
w0 = World(myagents,myspace,p,0.)
@time sim = run!(w0,Gillepsie(),tend)
```
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This is the simplest run you can do. Now time to more interesting things

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## Analysis
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### Size of the world
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Let's verify that the population's growth is logistic. We will plot the population size over time.
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To do so, one need to define `dt_saving` < `tend` to save every `dt_saving` time steps of the world.
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```julia
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myagents = [Agent(wholespace,(5,),ancestors=true,rates=true) for i in 1:K0/nodes]
w0 = World(myagents,wholespace,p,0.) # we need to reinitialise the world
@time sim = run!(w0,Gillepsie(),tend,dt_saving=2.)
wsize = [length(w) for w in sim[:]]
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using Plots
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Plots.plot(get_tspan(sim),wsize,
                label = "",
                ylabel = "Metapopulation size",
                xlabel ="time",
                grid = false)
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```
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![](tutorials/delta_comp_wsize.png)

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!!! notes "Callbacks"
    Note that one could also use a callback function to obtain time series of size of the world computed at simulation time. See [Simulation page](../manual/simulation.md).
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### Position through time

One might be tempted to plot the agents position for some time steps.

```julia
Plots.plot(sim,
        label = "",
        ylabel = "Geographical position",
        grid = false,
        markersize = 10)
```
![](tutorials/delta_comp_pos.png)