GenTimeDist: Calculates temperature dependent generation time distribution

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

Description

Function to produce matrix of generation time distribution that depends on temperature. For details, see the reference Codeco et al (2018).

Usage

GenTimeDist(serTemp, cid10 = "A90", GT.max = 10, smooth = "sinusoidal", nc = 1)

Arguments

serTemp	: Temperature series
cid10	"A90" for dengue (default), "A92": chikungunya, "A92.8": zika.
GT.max	: maximum number of weeks to consider for generation time
smooth	"sinusoidal" (default) or "raw"

Value

matrix with generation time distributions per week, one row per week, one column per SE.

References

Codeco et al (2018) https://doi.org/10.1016/j.epidem.2018.05.011

Examples

cli = getWU(stations = 'SBGL', vars=c("temp_med"), datasource=con) %>%
     mutate(temp_med = nafill(temp_med, rule = "arima")) 
gt <- GenTimeDist(cli$temp_med[1:50])
contour(gt, ylab="time", xlab="generation time (week)")

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