Skip to contents

Trace Plot Diagnostics

Source: R/plot_jags_tracedx.R
plot_jags_trace.Rd

plot_jags_trace() takes a list output from run_mod() to create trace plots for each chain run in the mcmc estimation. Defaults will produce every combination of antigen/antibody, parameters, and stratifications, unless otherwise specified. Antigen/antibody combinations and stratifications will vary by analysis. The antibody dynamic curve includes the following parameters:

  • y0 = baseline antibody concentration

  • y1 = peak antibody concentration

  • t1 = time to peak

  • r = shape parameter

  • alpha = decay rate

Usage

plot_jags_trace(
  data,
  iso = unique(data$curve_params$Iso_type),
  param = unique(data$curve_params$Parameter_sub),
  strat = unique(data$curve_params$Stratification)
)

Arguments

data

A list outputted from run_mod().

iso

Specify character string to produce plots of only a specific antigen/antibody combination, entered with quotes. Default outputs all antigen/antibody combinations.

param

Specify character string to produce plots of only a specific parameter, entered with quotes. Options include:

  • alpha = posterior estimate of decay rate

  • r = posterior estimate of shape parameter

  • t1 = posterior estimate of time to peak

  • y0 = posterior estimate of baseline antibody concentration

  • y1 = posterior estimate of peak antibody concentration

strat

Specify character string to produce plots of specific stratification entered in quotes.

Value

A list of ggplot2::ggplot objects producing trace plots for all the specified input.

Author

Sam Schildhauer

Examples


data <- serodynamics::nepal_sees_jags_post

# Specifying isotype, parameter, and stratification for traceplot.
plot_jags_trace(
                data = data,
                iso = "HlyE_IgA",
                strat = "typhi")