plot_seromodel: Visualise results of the provided model

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

Visualise results of the provided model

Description

Visualise results of the provided model

Usage

plot_seromodel(
  seromodel,
  serosurvey,
  alpha = 0.05,
  bin_serosurvey = FALSE,
  bin_step = 5,
  foi_df = NULL,
  foi_max = NULL,
  loo_estimate_digits = 1,
  central_estimate_digits = 2,
  seroreversion_digits = 2,
  rhat_digits = 2,
  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
alpha	1 - alpha indicates the credibility level to be used
bin_serosurvey	If TRUE, serodata is binned by means of prepare_bin_serosurvey. Otherwise, age groups are kept as originally input.
bin_step	Integer specifying the age groups bin size to be used when bin_serosurvey is set to TRUE.
foi_df	Dataframe with columns year/age Year/Age (depending on the model) foi Force-of-infection values by year/age
foi_max	Max FoI value for plotting
loo_estimate_digits	Number of loo estimate digits
central_estimate_digits	Number of central estimate digits
seroreversion_digits	Number of seroreversion rate digits
rhat_digits	Number of rhat estimate digits
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

seromodel summary plot

Examples

data(veev2012)
seromodel <- fit_seromodel(veev2012, iter = 100)
plot_seromodel(seromodel, veev2012)

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