Skip to contents

Plot convergence diagnostics over time

Source: R/plot.R
plot.EpiStrainDynamics.diagnostics.Rd

Plots the R-hat or effective sample size of the log-incidence trajectory (log_incidence) against time, with one line per pathogen, so that convergence problems can be located in time and by pathogen. The threshold used by diagnose_model() is shown as a dashed line.

Usage

# S3 method for class 'EpiStrainDynamics.diagnostics'
plot(x, metric = c("rhat", "n_eff"), xlab = "Time", ...)

Arguments

x

Output of diagnose_model(), of class EpiStrainDynamics.diagnostics

metric

The diagnostic to plot: "rhat" (default) or "n_eff"

xlab

Time label for x axis, defaults to "Time"

...

Not used

Value

ggplot2 plot output

Details

R-hat is shown between 1 and 1.2, so values far above the threshold run off the top of the plot. Effective sample size is shown on a log scale, covering the range of the values and the threshold, so that values near the threshold stay readable even when others are in the thousands.

Only the trajectory is plotted. Other parameters, including the spline coefficients of p-spline models, are listed in the parameters table of the diagnose_model() output.

Examples

if (FALSE) { # interactive()
mod <- construct_model(
  pathogen_structure = single(
    data = sarscov2,
    case_timeseries = "cases",
    time = "date"
  ),
  method = random_walk()
)
fit <- fit_model(mod)
diag <- diagnose_model(fit)
plot(diag)
plot(diag, metric = "n_eff")
}