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MODULE 1: SIR Model Basics
Introduction to Compartmental Models for Infectious Disease -
Introduction to Ordinary Differential Equations (ODEs) and the SIR Model
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Introduction to SIR Modelling in R
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MODULE 2: SIR Model ExtensionsModelling Density-dependent vs. Frequency-dependent Transmission
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SIR model with Demographics
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CASE STUDY: Modelling with Real-World DataSEIR & SEIRW models for Hepatitis E Virus (HEV) Outbreaks: A Case Study
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MODULE 3: Epidemic ThresholdsThe Basic Reproduction Number (R0)
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The Effective Reproduction Number (Re)
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Vaccination and Herd Immunity
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Practical Example: Models for Infectious Disease Management & PolicyVaccination Strategies to Control Hepatitis E Outbreaks: A Modeling Study (Cooper et al. 2018)
Lesson Video
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Lesson Code & Data
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got this ODE option, why don’t we have the N factored in ours
seir_model <- function(time, state, parameters) { with(as.list(c(state, parameters)), { N <- S + E + I + R dS <- -beta * S * I / N dE <- beta * S * I / N - sigma * E dI <- sigma * E - gamma * I dR <- gamma * I list(c(dS, dE, dI, dR)) }) }Wow, this makes modelling seem less intimidating. I have a question: Is it always necessary to plot all 3 graphs in the SIR model or just the “Infected” curve would be enough?
Glad to hear that you are enjoying the course! There is no need to plot all 3 curve every time, you can feel free to focus on the Infected curve. We usually plot all three just to inspect model outputs.
Thanks