GMRF_SEIJR_plot_Rt: Plot reproduction number through time from a SEIJR trajectory...

In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses

Description

Plot reproduction number through time from a SEIJR trajectory sample

Usage

GMRF_SEIJR_plot_Rt(
  trajdf,
  logdf,
  gamma0 = 73,
  gamma1 = 121.667,
  date_limits = c(as.Date("2020-02-01"), NA),
  path_to_save = "Rt.png",
  changePoints = c(2020.123, 2020.161, 2020.199, 2020.238),
  ...
)

Arguments

logdf	Either a dataframe or a path to rds containing a data frame with posterior logs
gamma0	rate of becoming infectious during incubation period
gamma1	rate of recovery once infectious
date_limits	a 2-vector containing bounds for the plotting window. If the upper bound is missing, will use the maximum time in the trajectories
path_to_save	Will save a png here
changePoints	the time where beta changes

Value

a list with derived outputs from the trajectories. The first element is a ggplot object if you want to further customize the figure

emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 a.m.