Disruption-of-Vector-Host-Preference

Python implementation of the population dynamics proposed in the paper: "Disruption of Vector Host Preference with Plant Volatiles May Reduce Spread of Insect-Transmitted Plant Pathogens".

Paper Error

I noticed there is an error in the original paper in equation 2. The correct equation should be:

$$ \frac{dP_i}{dt} = a I_i + c \lambda_u P_u T_i - (1 - c) p P_i T_u - \mu_a P_i $$

Tutorial

Follow the steps below to set up the environment and run the model to replicate the figures from the paper.

Setup

1. Clone the repository:

   git clone https://github.com/gianluccacolangelo/Disruption-of-Vector-Host-Preference
   cd Disruption-of-Vector-Host-Preference

2. Install dependencies using Conda:

   Make sure you have Conda installed. If not, you can install Miniconda.

   conda env create -f conda_environment.yml

3. Activate the environment:

   conda activate Disruption-of-Vector-Host-Preference

Usage

After setting up the environment, you can start using the model to simulate the population dynamics.

1. Open a Python session:

   python

2. Import and use the PsyllidModel class:

   from model import PsyllidModel
   
   # Create an instance of the model with default parameters
   model = PsyllidModel()
   
   # Solve the model
   model.solve()
   
   # Plot the results
   model.plot()

Customizing the Model

You can change the parameters to see how different conditions affect the population dynamics. For example:

# Modify critical parameters
model = PsyllidModel(c=0.5, lambdu=0.06, gamma=17e-8, g=56, beta=0.04, initial_conditions=[0, 1, 0, 0, 13000, 0])

# Solve and plot the modified model
model.solve()
model.plot()

Example

Here is an example of how to create, solve, and plot the model:

from model import PsyllidModel

# Initialize the model with specific parameters
model = PsyllidModel(c=0.75,mua=7.6,lambdu=0.06, gamma=17e-8, g=56, beta=0.04, initial_conditions=[0, 1, 0, 0, 13000, 0])

# Solve the model
model.solve()

# Plot the results
model.plot()

Environment Details

The environment is defined in the conda_environment.yml file, which includes all necessary dependencies:

name: Disruption-of-Vector-Host-Preference
channels:
  - defaults
dependencies:
  - python=3.8
  - matplotlib
  - numpy
  - scipy

Contributing

Contributions are welcome! Please feel free to submit a pull request or open an issue.

---