baclava (version 1.0)

plot.baclava: Plot Posterior Distribution Parameters

Description

Convenience function to facilitate exploration of posterior distributions through trace plots, autocorrelations, and densities, as well as plotting the estimated hazard for transitioning to the preclinical compartment.

Usage

# S3 method for baclava
plot(
  x,
  y,
  ...,
  type = c("density", "trace", "acf", "hazard"),
  burnin = 0L,
  max_age = 90L,
  trace_var = c("psi", "rate_H", "rate_P", "beta")
)

Value

A gg object

Arguments

x

An object of class baclava.

y

Ignored

...

Ignored

type

A character object. One of {"density", "trace", "acf", "hazard"}. The type of plot to generate

burnin

An integer object. Optional. The number of burn-in samples. Used only for type = "trace". One trace plot is generated for the burnin iterations; a second for the post-burnin iterations. Note, this refers to the number of kept (thinned) samples.

max_age

A numeric object. For type = "hazard", the maximum age at which to evaluate the hazard.

trace_var

A character object. The parameter for which trace plots are to be generated. Must be one of {"psi", "rate_H", "rate_P", "beta"}

Examples

data(screen_data)

theta_0 <- list("rate_H" = 7e-4, "shape_H" = 2.0,
                "rate_P" = 0.5  , "shape_P" = 1.0,
                "beta" = 0.9, psi = 0.4)
prior <- list("rate_H" = 0.01, "shape_H" = 1,
              "rate_P" = 0.01, "shape_P" = 1,
              "a_psi" = 1/2 , "b_psi" = 1/2,
              "a_beta" = 38.5, "b_beta" = 5.8)

# This is for illustration only -- the number of Gibbs samples should be
# significantly larger and the epsilon values should be tuned.
example <- fit_baclava(data.assess = data.screen,
                       data.clinical = data.clinical,
                       t0 = 30.0,
                       theta_0 = theta_0,
                       prior = prior)
                       
plot(example)
plot(example, type = "trace", trace_var = "psi", burnin = 0L) 
plot(example, type = "trace", trace_var = "rate_H", burnin = 0L) 
plot(example, type = "trace", trace_var = "rate_P", burnin = 0L) 
plot(example, type = "trace", trace_var = "beta", burnin = 0L) 
plot(example, type = "acf")
plot(example, type = "hazard", max_age = 70)