Commit fc95ad1b authored by bvictor's avatar bvictor
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Update README.md

parent 07e3153e
......@@ -16,49 +16,7 @@ Pkg.add("ABMEv#no_C_matrix")
```julia
using ABMEv
```
To develop, you can add the dependencies in the project by doing
```julia
using Pkg
Pkg.activate("path_to_ABMEv")
```
## Birth and Death mechanisms
> We are always balanced between taking the integral of the competition and resource kernel as constant, or taking its maximum peak as constant.
:poop:
## Geotrait
The geotrait is calculated *a posteriori*, and is not taken into account during the simulation.
> It used to be but for the sake of simplicity we now forget about it.
### Mutation
If anisotropy in mutation, the following parameters should be declared as arrays where each entry corresponds to a dimension.
- ```mu``` The probability of mutation.
- ```D``` If mutation happens on the agent, the increment follows $\mathcal{N}_{ 0, D}$
### Birth
#### Growth
- Resource kernel for agent with trait $x$ is defined as
```math
K_{\mu,\sigma}(x) = K_0 \mathcal{N}_{\mu,\sigma}(x)
```
with $\mu$ and $\sigma$ potentially vectors.
> We just modified this in ABMEv_Agent.jl so you should check if it works.
- Dirth coefficient is defined as $`b(x) = K(x)`$
### Death
#### Competition
- Competition between agent with trait ```x``` and ```y``` is defined as
```math
\alpha(x,y) = \exp(-\sum_i^{N(t)} \frac{1}{\sigma_{\alpha_i}^{n_\alpha}}\sum_j^T (x_{i,j} - y_{i,j})^{n_\alpha})
```
- Death coefficient is defined as $`d(x^{(i)}) = \sum_j^{N(t)} \alpha(x^{(i)},x^{(j)})`$
> We are not sure if the sum includes $`x^{(i)}`$ or not.
### Fitness
Fitness is defined as ```b - d```.
## Parameter description
- ```K0``` Carrying capacity
- ```a``` only used for mode ```grad2D``` where growth rate is set such as $`\mu = a x_1`$
> We are not sure if this is OK or not? Check it
[Grad2D kernel explained](https://gitlab.ethz.ch/bvictor/abmev/-/wikis/Grad2D)
### Gillepsie algorithm
```julia
......@@ -104,6 +62,35 @@ You have several options available concerning the resource implemented and compe
- ``` mode="split"``` corresponds to a scenario where the resource is splitted in two
- ``` mode="graph"``` this guy is probably not working
### Mutation
If anisotropy in mutation, the following parameters should be declared as arrays where each entry corresponds to a dimension.
- ```mu``` The probability of mutation.
- ```D``` If mutation happens on the agent, the increment follows $\mathcal{N}_{ 0, D}$
### Birth
#### Growth
- Resource kernel for agent with trait $x$ is defined as
```math
K_{\mu,\sigma}(x) = K_0 \mathcal{N}_{\mu,\sigma}(x)
```
with $\mu$ and $\sigma$ potentially vectors.
> We just modified this in ABMEv_Agent.jl so you should check if it works.
- Dirth coefficient is defined as $`b(x) = K(x)`$
### Death
#### Competition
- Competition between agent with trait ```x``` and ```y``` is defined as
```math
\alpha(x,y) = \exp(-\sum_i^{N(t)} \frac{1}{\sigma_{\alpha_i}^{n_\alpha}}\sum_j^T (x_{i,j} - y_{i,j})^{n_\alpha})
```
- Death coefficient is defined as $`d(x^{(i)}) = \sum_j^{N(t)} \alpha(x^{(i)},x^{(j)})`$
> We are not sure if the sum includes $`x^{(i)}`$ or not.
### Fitness
Fitness is defined as ```b - d```.
## Parameter description
- ```K0``` Carrying capacity
- ```a``` only used for mode ```grad2D``` where growth rate is set such as $`\mu = a x_1`$
> We are not sure if this is OK or not? Check it
[Grad2D kernel explained](https://gitlab.ethz.ch/bvictor/abmev/-/wikis/Grad2D)
### Parallelism
You can run your script in parallel, which makes sense for large populations. To do so:
......@@ -147,6 +134,16 @@ You can specify what you want to plot in the array ```what```:
- ```3d``` plots a 3d diagram with first and second component as x and y axis
- ```var``` plots the variance of the component specified by ```trait=2```
- ```vargeo``` plots the variance of the geotrait
## Developping the code
I recommend to first clone your branch in the directory you like best, and then to
To develop, you ca
```julia
using Pkg
Pkg.dev("path_to_ABMEv_dir")
```
You can also do the same trick with directly the gitlab address, cf [https://docs.julialang.org/en/v1/stdlib/Pkg/index.html](Pkg.jl)
## References
- [Champagnat and Ferriere founding article](https://linkinghub.elsevier.com/retrieve/pii/S0040580905001632)
- [Champagnat and Ferriere second article - 2008](https://www.tandfonline.com/doi/full/10.1080/15326340802437710)
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