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Modelling marine diseases with ordinary differential equations using Matlab, [2021/11][eng]
LECTURE MATERIALS
Lesson 5: Formulation of the basic reproduction number (Ro) of a contact-based model
Lesson 5: Formulation of the basic reproduction number (Ro) of a contact-based model
Completion requirements
Click
LESSON 5 Ro FINAL_SID.pdf
link to view the file.
Previous activity
LESSON 4.2: MATLAB code for the SID model
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SYLLABUS
Lesson 1: Basic Concepts of marine disease transmission
Lesson 2: Introduction to MATLAB for marine disease modelling
Lesson 3: Matlab instructions to build up and run marine disease models
Lesson 4: Building up a contact-based marine disease transmission model
Lesson 4.1: Matlab codes for the SI model
LESSON 4.2: MATLAB code for the SID model
Lesson 6: Sensitivity analysis of marine disease models (SI and SID models)
1. MARINE DISEASE ECOLOGY (BOOK)
2. An Introduction to Infectious disease Modelling (Book)
3. Themed Issue: Marine disease. Philosophical Transactions on the Royal Society B, Biological Sciences.
4. Parasite Ecology
5. Introduction to MATLAB programming CourseWare
6. GNU OCTAVE. An open source software, alternative to MATLAB.
7. Generalized SEIR Epidemic Model (fitting and computation). MATLAB: Central. File Exchanges.
8. SEIRS Epidemic Model. MATLAB Central. File Exchange.
9. Ro formulation using the Next Generation Matrix (Diekmann et al. 2010)
10. Sensitivity Analysis of Infectious Disease Models
11. Calc (LibreOffice). An open source software, alternative to Excel.
12. Graphical User Interface (GUI) for marine disease modelling. MATLAB: Central. File Exchanges.
EXERCISE 1: Build up models for marine disease transmission through contact with environmental pathogens
Solution to Exercise 1: ODEs for SIP and SIPD models and models' description
Solution to Exercise 1: MATLAB code for the SIP model
Solution to Exercise 1: MATLAB code for the SIPD model
EXERCISE 2: Formulation of Ro for SIP and SIPD models
Solution to Exercise 2: Formulation of Ro for SIP and SIPD models
EXERCISE 3: Build up models for marine disease transmission through filtration of environmental pathogens
Solution to Exercise 3: ODEs for SIPF and SIPDF models and models' description
Solution to Exercise 3: MATLAB code for the SIPF model
EXERCISE 4: Formulation of Ro for SIPF and SIPFD models
Solution to Exercise 4: Formulation of Ro for SIPF and SIPDF models
EXERCISE 5: Sensitivity analisis (SA) of Ro for SIP, SIPD, SIPF and SIPDF models
Solution to Exercise 5: Sensitivity analisis (SA) of Ro for SIP, SIPD, SIPF and SIPDF models
Self-Evaluation EXERCISE 1: Build up a SEIR model
Solution to Self-Evaluation Exercise 1: MATLAB code for the SEIR model
Self-Evaluation EXERCISE 2: Build up the SIPDB model
Solution to Self-Evaluation Exercise 2: MATLAB code for the SIPDB model
SELF-Evaluation EXERCISE 3: Running simulations using the Graphical User Interface (GUI) for marine disease modelling
Self-Evaluation EXERCISE 3: Matlab files for using the GUI
Download the GUI from the MATLAB Central, File Exchanges.
Teachers and affiliations
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Lesson 6: Sensitivity analysis of marine disease models (SI and SID models)
