bdsky_plot: Plot Birth_Death Skyline Plots

In BEAST2-Dev/rbeast2:

Description

This function plots the epidemiological parameters of a BDSKY analysis with their HPD intervals.

Usage

bdsky_plot(logs = NULL, burninpercent = 10, recent = NULL,
  gridSize = 20, RepNumb = "reproductiveNumber",
  bUninfectiousRate = "becomeUninfectiousRate.s",
  sProportion = "samplingProportion.s", SamplingDates = NULL)

Arguments

logs	(character) The path to the log file(s) or the path to the file with ".txt" extension that stores the path to all log files to be analyzed or NULL to select (default: NULL)
burninpercent	(integer) The percentage of samples that should be ignored from the log file
recent	(numeric) Date of the most recent sample (for plotting from past to present)
gridSize	(integer)
RepNumb	(character) Name of the R0 parameter (default: "R0.s")
bUninfectiousRate	(character) Name of the becomeUninfectious parameter (default: "becomeUninfectiousRate.s")
sProportion	(character) Name of the samplingProportion parameter (default: "samplingProportion.s")
SamplingDates	(numeric) If specific times were used to set the changes in samplingProportion (using the parameter samplingRateChangeTimes in the xml file), the dates of the changes in the rate, otherwise NULL (default)

Details

Currently, specific times can only be used for samplingProportion (using the parameter samplingRateChangeTimes in the xml file) and must be provided (in the xml file) in order from the oldest to the most recent.

Value

A PDF with the plots

Author(s)

Denise Kuehnert ([e-mail])

Carlo Pacioni ([e-mail])

BEAST2-Dev/rbeast2 documentation built on May 5, 2019, 10:24 a.m.