build_stan_data: Builds stan data for sampling depending on the selected model

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

Builds stan data for sampling depending on the selected model

Description

Builds stan data for sampling depending on the selected model

Usage

build_stan_data(
  serosurvey,
  model_type = "constant",
  foi_prior = sf_uniform(),
  foi_index = NULL,
  is_log_foi = FALSE,
  foi_sigma_rw = sf_none(),
  is_seroreversion = FALSE,
  seroreversion_prior = sf_none()
)

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"
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_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
is_log_foi	Boolean to set logarithmic scale in the FoI
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.
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

Value

List with necessary data for sampling the specified model

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