CFR plot based on aggregate data

cfr_calc

# Define delay params
param_1 <- log(5)
param_2 <- 1

# Onsets at time 0
initial_onsets <- 100

# CFR
cfr <- 0.5

# Formula
# E(deaths by time t) = CFR x cases with known outcome by time t if outcome were fatal

# Calculate number of known fatal outcomes on day 10
day_10_deaths <- initial_onsets*plnorm(10, param_1, sdlog = param_2)

# Plot
time_range <- 0:30

plot(time_range,initial_onsets*cfr*plnorm(time_range, param_1, sdlog = param_2),
     ylim=c(0,initial_onsets),
     xlim=c(0,max(time_range)),
     yaxs="i",xaxs="i",xlab="day",ylab="events")
lines(c(0,50),initial_onsets*cfr*c(1,1),lty=2)

points(time_range,initial_onsets*plnorm(time_range, param_1, sdlog = param_2),col="pink")
points(10,day_10_deaths,col="red")

text(x=11,y=day_10_deaths,"estimated fatal outcomes/CFR",adj=0,col="red")
text(x=10,y=30,"cumulative deaths",adj=0)

lines(c(10,10),c(0,day_10_deaths),col="red")