MarineEpi

This toolbox provides a graphical user interface (GUI) for teaching and research in marine pathogen transmission modelling

45 Downloads

Updated 19 Jul 2022

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MarineEpi

MarineEpi modelling file is presented to the end user in the MarineEpi GUI. The user can take advantage of all of the features of MarineEpi to model different host-pathogen systems, run different marine disease scenarios and obtain information about disease dynamics displaying plots for S, I, P, DI, prevalence of infection and mortality (see model variables decription below).

Description

This toolbox provides a graphical user interface (GUI) for modelling different marine host-pathogen systems. The first version of this GUI was created for the RCN Marine Disease Modeling and Transmission Workshop 2015. This GUI is based on the previously developed marine disease models (Bidegain et al. 2016). The models and this GUI were created by Gorka Bidegain, Tal Ben-Horin, John Klinck, Eric Powell, Eileen Hofmann.

Installing the toolbox and opening the GUI

The user needs to find in Matlab Add-ons the MarineEpi toolbox and add it to Matlab and open the created folder. The folder should have the following files: MarineEpi.m, MarineEpi.fig.

Alternatively, the user can download the toolbox from this link:

View MarineEpi on File Exchange

Once Matlab is working in this folder the MarineEpi user interface will be opened by typing MarineEpi in the command window. Alternatively, the user can open the GUI from the Editor window. For this, first the user will select the file MarineEpi.m file located in the working folder by clicking twice on the file. Once this file is selected in the Editor window the user wil open the GUI by clicking on the RUN button.

Features

This GUI-based toolbox was develped for modelling different marine host-pathogen systems and running model scenarios with different initial conditions and model parameters. MarineEpi users can generate an SI model, where pathogen transmission occurs through contact of Susceptible individuals (S) with infected individuals (I), an SID model where transmission occurs through contact of S with dead infected individuals (DI), an SIP model, where transmission occurs through contact of S with environmental pathogens (IP) released by infected individuals, and an SIPD model, where transmission occurs through contact of S with IP. The user can run simulations with any of these models by giving specific values to some model parameters (see parameter description in the section "Parameters").

Model variables:

S=Susceptibles I=Infected DI=Dead Infected IP=Infective Particles

Model parameters:

Iinfect=infection rate by contact with Infected animals (infected produced/Infected animal * day) Dinfect=infection rate by contact with Dead Infected animals (infected produced/Dead animal * day) IPinfect=infection rate by contact with Infective Particles animals (infected produced/Particles*day) Imort=mortality rate of infected (1/day) Bmort=background mortality rate (1/day) DeadDecay=Removal reate of dead animals (scavenging,decomposition...) (1/day) Irelease=Infectious particles released by Infected (particles/animal/day) Drelease=Infectious particles released by Dead Infected (particles/animal/day) IPremove=Removal rate of Infectious Particles form the environment by advecion, inactivation, difussion...(particles/animal/day)

References

Bidegain, G., Powell, E. N., Klinck, J. M., Ben‐Horin, T., & Hofmann, E. E. (2016). Marine infectious disease dynamics and outbreak thresholds: contact transmission, pandemic infection, and the potential role of filter feeders. Ecosphere, 7(4), e01286.

Cite As

Bidegain, G., Ben-Horin, T., Powell, E.E., Klinck, J.M., Hoffman, E.E. (2021). MarineEpi: A Graphical User Interface for marine disease modeling (https://www.https://mathworks.com/matlabcentral/fileexchange/87999-marineepi), MATLAB Central File Exchange.

MATLAB Release Compatibility
Created with R2018a
Compatible with any release
Platform Compatibility
Windows macOS Linux
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Version Published Release Notes
4.2

See release notes for this release on GitHub: https://github.com/gbidegain/MarineEpi/releases/tag/4.2

4.1

description

3.1

title

2.1

Changes in figure file

2.0

Description

1.9

Description

1.8

citation

1.6

summary

1.5

files

1.4

Files

1.3

files

1.2

new file

1.1

Title

1.0.7

Edits

1.0.6

Cite as corrected

1.0.5

Authors, correction

1.0.4

Citation

1.0.3

Changes on title text

1.0.2

Added a new citation form

1.0.1

Image included

1.0.0

To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.