I created a R code below and try to create similar curve for "Susceptible, Infected, and Recovered", like the third graph here: https://penn-chime.phl.io/

But, I don't know how to determine the parameters beta, gamma and others. Can anyone help to generate those parameter based on the information provided from the website? Thank you.

install.packages(deSolve)

library(deSolve)

# writing the differential equations in R

sir_equations<- function(time, variables, parameters) {

with(as.list(c(variables, parameters)), {

dS<- -beta * I * S

dI<- beta * I * S - gamma * I

dR<- gamma * I

return(list(c(dS, dI, dR)))

})

}

# defining some value for the parameters

parameters_values<- c(

beta = 0.001, # infectious contact rate (/person/day)

gamma = 0.015 # recovery rate (/day)

)

# initial values for the variables

initial_values<- c(

S=3599733, # number of susceptibles at time = 0

I=266, # number of infectious at time =0

R=0 # number of recovered (and immune) at time=0

)

time_values<- seq(0, 125) # days

# ode() function

sir_values_1 <- ode(

y = initial_values,

times = time_values,

func = sir_equations,

parms = parameters_values

)

sir_values_1 <- as.data.frame(sir_values_1)

# plot

with(sir_values_1, {

plot(time, S, type = "l", col = "blue", xlab = "time (days)", ylab = "number of people")

lines(time, I, col = "red")

lines(time, R, col = "darkgreen")

})

legend("right", c("susceptibles", "infectious", "recovered"),

col = c("blue", "red", "darkgreen"), pch = 1, bty = "n")