gmrf_exogsir_plot_size: Plot the cumulative infections through time from a SEIJR...

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

Description

Plot the cumulative infections through time from a SEIJR trajectory sample

Usage

gmrf_exogsir_plot_size(
  trajdf,
  case_data = NULL,
  date_limits = c(as.Date("2020-02-01"), NA),
  path_to_save = "size.png",
  log_y_axis = F,
  k = 0.16,
  ...
)

Arguments

case_data	An optional dataframe containing reported/confirmed cases to be plotted alongside estimates. *Must* contain columns 'Date' and 'Cumulative'. 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
log_y_axis
k	Overdispersion parameter (default 16 per cent, Lloyd Smith 2005)

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.