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