Rtoriginal: Computes the effective reproductive number using a Alerta's...

In claudia-codeco/AlertTools: utility functions for the Alerta Dengue System

Description

Calculates the effective reproductive number from the growth rate of cases. The The original formulation is simply the ratio between 3-weeks accumulated cases at week (t+1) and the 3-weeks accumulated cases at week t.

Usage

Rtoriginal(
  obj,
  count = "casos",
  meangt,
  CI = "beta",
  alpha = 0.95,
  a0 = 2,
  b0 = 3
)

Arguments

obj	object with the format of getcases. A data.frame with variables "casos" and "SE".
count	case counts (adjusted or nonadjusted incidence).
meangt	the exact period between primary and secondary infections
CI	Model used to compute the confidence interval. "beta" is the only choice.

Value

data.frame with estimated Rt and confidence intervals

Examples

res = getCases(city = c(330455), withdivision = FALSE) # Rio de Janeiro
# Rt original
rt<-Rtoriginal(obj = res, count = "casos", meangt=3)
plot(rt$Rt, type="l", xlab = "weeks", ylab = "Rt")
lines(rt$lwr,lty=3)
lines(rt$upr,lty=3)
abline(h = 1, col = 2)

claudia-codeco/AlertTools documentation built on Aug. 12, 2021, 9:58 a.m.