fit_seromodel: Runs specified stan model for the Force-of-Infection (FoI)

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

Runs specified stan model for the Force-of-Infection (FoI)

Description

Runs specified stan model for the Force-of-Infection (FoI)

Usage

fit_seromodel(
  serosurvey,
  model_type = "constant",
  is_log_foi = FALSE,
  foi_prior = sf_normal(),
  foi_sigma_rw = sf_none(),
  foi_index = NULL,
  foi_init = NULL,
  is_seroreversion = FALSE,
  seroreversion_prior = sf_normal(),
  ...
)

Arguments

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
model_type	Type of the model. Either "constant", "age" or "time"
is_log_foi	Boolean to set logarithmic scale in the FoI
foi_prior	Force-of-infection distribution specified by means of the helper functions. Currently available options are: sf_normal Function to set normal distribution priors sf_uniform Function to set uniform distribution priors
foi_sigma_rw	Prior distribution for the standard deviation of the Force-of-Infection. Currently available options are: sf_normal Function to set normal distribution prior. Available for time models in the log-scale sf_cauchy Function to set Cauchy distribution prior. Available for time models in regular scale.
foi_index	Integer vector specifying the age-groups for which Force-of-Infection values will be estimated. It can be specified by means of get_foi_index
foi_init	Initialization function for sampling. If null, default is chosen depending on the foi-scale of the model
is_seroreversion	Boolean specifying whether to include seroreversion rate estimation in the model
seroreversion_prior	seroreversion distribution specified by means of the helper functions. Currently available options are: sf_normal Function to set normal distribution priors sf_uniform Function to set uniform distribution priors sf_none Function to set no prior distribution
...	Additional parameters for rstan

Value

stan_fit object with Force-of-Infection and seroreversion (when applicable) samples

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
)

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