serofoi (version 1.0.3)

fit_seromodel: 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(),
  ...
)

Value

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

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

Examples

# \donttest{
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
)
# }