plot_trace: make a trace plot of a single fitted variable

In ada-w-yan/deltaomicron1: Fit model to Delta and Omicron growth curves with and without Camostat

make a trace plot of a single fitted variable

Description

make a trace plot of a single fitted variable

Usage

plot_trace(
  chain,
  true_value,
  start_value,
  var_name,
  y_lab,
  ylim,
  zoom,
  n_samples = 0,
  real_data
)

Arguments

chain	data table containing iterations of MCMC chain after discarding burn-in
true_value	numeric vector of length 1. The true parameter value (if unknown because we're using real data, set this to any value)
start_value	Parameter value at start of MCMC chain (before discarding burn-in)
var_name	name of parameter to plot in colnames(chain)
y_lab	parameter name to display on plot
ylim	if zoom = FALSE, numeric vector of length 2 giving lower and upper limits of y axis. If either of these is NA, the range of the parameter values in the chain + the start value is used. if zoom = TRUE, this parameter is not used.
zoom	logical vector of length 1. if TRUE, the y-axis limits are the range of the parameter values in the chain (the start value is disregarded). if FALSE, the limits are as descibed in ylim.
n_samples	numeric vector of length 1. number of samples to plot, taken at evenly spaced intervals along the chain. if 0, plot all samples.

Value

ggplot object

ada-w-yan/deltaomicron1 documentation built on June 24, 2022, 5:41 a.m.