inst/doc/earlyR.R

In earlyR: Estimation of Transmissibility in the Early Stages of a Disease Outbreak

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.align = "center",
  fig.width = 7,
  fig.height = 5
)

## ----data---------------------------------------------------------------------

onset <- as.Date(c("2017-02-04", "2017-02-12", "2017-02-15",
                   "2017-02-23", "2017-03-01", "2017-03-01",
		   "2017-03-02", "2017-03-03", "2017-03-03"))		 


## ----incidence----------------------------------------------------------------

library(incidence)
i <- incidence(onset)
i
plot(i, border = "white")


## ----incidence2---------------------------------------------------------------

today <- as.Date("2017-03-21")
i <- incidence(onset, last_date = today)
i
plot(i, border = "white")


## ----si-----------------------------------------------------------------------

mu <- 15.3 # mean in days days
sigma <- 9.3 # standard deviation in days


## ----estimate-----------------------------------------------------------------

library(earlyR)
library(ggplot2)

res <- get_R(i, si_mean = mu, si_sd = sigma)
res
plot(res)

plot(res, "lambdas", scale = length(onset) + 1) +
  geom_vline(xintercept = onset, col = "grey", lwd = 1.5) +
  geom_vline(xintercept = today, col = "blue", lty = 2, lwd = 1.5)


## ----sample_R-----------------------------------------------------------------

R_val <- sample_R(res, 1000)
summary(R_val)
quantile(R_val)
quantile(R_val, c(0.025, 0.975))
hist(R_val, border = "grey", col = "navy",
     xlab = "Values of R",
     main = "Sample of likely R values")


## ----generate_si--------------------------------------------------------------

si <- res$si
si


## ----projections--------------------------------------------------------------

library(projections)

future_i <- project(i, R = R_val, n_sim = 1000, si = res$si, n_days = 30)
future_i
mean(future_i) # average incidence / day
plot(future_i)


## ----pred_size----------------------------------------------------------------

predicted_n <- colSums(future_i)
summary(predicted_n)
hist(predicted_n, col = "darkred", border = "white",
     main = "Prediction: new cases in 30 days",
     xlab = "Total number of new cases")


## ----alternative--------------------------------------------------------------

alt_i <- incidence(onset)
alt_res <- get_R(alt_i, si_mean = mu, si_sd = sigma)
alt_R_val <- sample_R(alt_res, 1000)
alt_future_i <- project(alt_i, R = alt_R_val, n_sim = 1000, si = res$si, n_days = 30)
alt_future_i
mean(alt_future_i)
plot(alt_future_i)

## alternative plot
col <- "#cc66991a"
matplot(alt_future_i, type = "l", col = col, lty = 1, lwd = 5,
        xlab = "Day from today",
	ylab = "Projected daily incidence")

alt_predicted_n <- colSums(alt_future_i)
summary(alt_predicted_n)
hist(alt_predicted_n, col = "darkred", border = "white",
     main = "Prediction: new cases in 30 days",
     xlab = "Total number of new cases")