Part 1 Solutions

Exercise 1

library(epiworldR)

# Initialize model
model_seir <- ModelSEIR("COVID-19", 
                        prevalence = 0.01, 
                        transmission_rate = 0.9,
                        recovery_rate = 1/4,
                        incubation_days = 4)

# Adding a small world population
agents_smallworld(
 model_seir,
 n = 10000,
 k = 5,
 d = FALSE,
 p = .01
 )
 
# Running model
run(model_seir, ndays = 100, seed = 1912)

_________________________________________________________________________
Running the model...
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
 done.

# Plotting
plot(model_seir)

# Day of peak infections 
x <- get_hist_total(model_seir)
which.max(x$counts[x$state == "Infected"]) - 1

[1] 12

# Number of infections on peak day
max(x$counts[x$state == "Infected"])

[1] 1010

Exercise 2

repnum <- get_reproductive_number(model_seir)
plot(repnum, type = 'b')