plot_Rt: Visualizing Time-varying reproductive numbers

In wenlab501/EpiTrans: R package for estimation of epidemic transmissibility in time and space

Visualizing Time-varying reproductive numbers

Description

Plot line chart of individual reproductive numbers by time

Usage

plot_Rt(
  t,
  Rt,
  Rt2 = NULL,
  percentile = c(0, 1),
  interval = c("day", "week", "month"),
  col = "orange",
  col2 = "darkgreen",
  label = "Rt",
  label2 = "Rt2"
)

Arguments

t	Vector of time of data points.
Rt	Vector of individual reproductive numbers of data points, stand for Rt1.
Rt2	Another vector of individual reproductive numbers of data points to compare, stand for Rt2.
percentile	A 2-length numerical vector, draw the area of value of percentile range; if c(0,1) means min and max will be drawn, c(0.05,0.95) means the middle 90 percent value will be drawn.
interval	Character; time resolution(day, week, month) of animation ; aggregrate data through day, week or month.
col	Color of line Rt1.
col2	Color of line Rt2.
label	Label of line Rt1.
label2	Label of line Rt2.

Examples

data("EpiTrans")

covid = GeoLocater(TimeDF = covid19,PointsDF = RndPts)
covid.R_adj=Rj(t = covid$date, x = covid$x, y = covid$y, GI.pdf = lpdf_GI(5.2,1.5), unit_coord = "meter")

plot_Rt(t = covid$date, Rt=covid.R_adj$Rj, Rt2=covid.R_adj$Rj,percentile = c(.025,.975))

wenlab501/EpiTrans documentation built on July 8, 2022, 9:14 a.m.