SEIJR_plot_daily_inf: Plot the daily new infections through time from a SEIJR...

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

Description

Plot the daily new infections through time from a SEIJR trajectory sample

Usage

SEIJR_plot_daily_inf(
  trajdf,
  logdf,
  case_data = NULL,
  date_limits = c(as.Date("2020-02-01"), NA),
  path_to_save = "daily.png",
  log_y_axis = F,
  ...
)

Arguments

logdf	Either a dataframe or a path to rds containing a data frame with posterior logs
case_data	An optional dataframe containing reported/confirmed cases to be plotted alongside estimates. *Must* contain columns 'Date' and 'Confirmed'. Ensure Date is not a factor or character (see as.Date )
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

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.