part2b.qmd

---
title: "Part 2 Solutions"
---

## Exercise

```{r, fig.height=10}
library(epiworldR)

# Initialize model
model_sir <- ModelSIRCONN(
  name              = "Flu",
  n                 = 10000, 
  prevalence        = 0.001, 
  contact_rate      = 2.1,
  transmission_rate = 0.5,
  recovery_rate     = 1/4
  )

# Building the virus
delta <- virus(name = "Delta", prob_infecting = .3, recovery_rate = 1/4)
# Adding the virus to the model
add_virus(model_sir, delta, .001)

# Building the masking tool
masking <- tool(name = "Masking",   
                susceptibility_reduction = 0.0,
                transmission_reduction   = 0.3, # Only transmission
                recovery_enhancer        = 0.0,
                death_reduction          = 0.0)
# Adding the tool to the model
add_tool(model_sir, masking, proportion = 0.6)

# Run the model and print summary
run(model_sir, ndays = 75, seed = 1912)
summary(model_sir)

# Reproductive number 
repnum <- get_reproductive_number(model_sir)

# Plotting
op <- par(mfrow = c(2,1))
plot(model_sir)
plot(repnum, type="b")
par(op)

# Day of peak infections 
x <- get_hist_total(model_sir)
which.max(x$counts[x$state == "Infected"]) - 1
# Number of infections on peak day
max(x$counts[x$state == "Infected"])
```