plot_rhats: Plot r-hats convergence criteria for the specified model

In serofoi: Bayesian Estimation of the Force of Infection from Serological Data

Plot r-hats convergence criteria for the specified model

Description

Plot r-hats convergence criteria for the specified model

Usage

plot_rhats(
  seromodel,
  serosurvey,
  size_text = 11,
  plot_constant = FALSE,
  x_axis = NA
)

Arguments

seromodel	stan_fit object obtained from sampling a model with fit_seromodel
serosurvey	survey_year Year in which the survey took place (only needed to plot time models) age_min Floor value of the average between age_min and age_max age_max The size of the sample n_sample Number of samples for each age group n_seropositive Number of positive samples for each age group
size_text	Size of text for plotting (base_size in ggplot2)
plot_constant	boolean specifying whether to plot single Force-of-Infection estimate and its corresponding rhat value instead of showing this information in the summary. Only relevant when seromodel@model_name == "constant")
x_axis	either "time" or "age". Specifies time axis values label for constant model additional plots. Only relevant when and seromodel@model_name == "constant"

Value

ggplot object showing the r-hats of the model to be compared with the convergence criteria (horizontal dashed line)

Examples

data(chagas2012)
seromodel <- fit_seromodel(
  serosurvey = chagas2012,
  model_type = "time",
  foi_index = data.frame(
    year = 1935:2011,
    foi_index = c(rep(1, 46), rep(2, 31))
  ),
  iter = 100,
  chains = 2
)
plot_rhats(seromodel, chagas2012)

serofoi documentation built on April 3, 2025, 11:40 p.m.