# Bayesian Estimation of the Force of Infection from Serological Data

## Documentation for package ‘serofoi’ version 1.0.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

serofoi-package | The 'serofoi' package.
add_age_group_to_serosurvey | Adds age group marker to serosurvey
build_stan_data | Builds stan data for sampling depending on the selected model
chagas2012 | Chagas seroprevalence data in serofoi
chik2015 | Chikungunya seroprevalence data in serofoi
extract_central_estimates | Extracts central estimates from stan_fit object for specified parameter
fit_seromodel | Runs specified stan model for the Force-of-Infection (FoI)
get_foi_index | Generates Force-of-Infection indexes for heterogeneous age groups
plot_foi_estimates | Plots Force-of-Infection central estimates
plot_rhats | Plot r-hats convergence criteria for the specified model
plot_seromodel | Visualise results of the provided model
plot_seroprev_estimates | Plot seroprevalence estimates on top of the serosurvey
plot_serosurvey | Plots seroprevalence from the given serosurvey
plot_summary | Plots model summary
prepare_serosurvey_for_plot | Prepares serosurvey for plotting
probability_exact_age_varying | Computes the probability of being seropositive when Forces-of-Infection (FoIs) vary by age
probability_exact_time_varying | Computes the probability of being seropositive when Forces-of-Infection (FoIs) vary by time
prob_seroprev_age_by_age | Generate probabilities of seropositivity by age based on an age-varying Force-of-Infection (FoI) model.
prob_seroprev_age_time_by_age | Generate probabilities of seropositivity by age based on an age-and-time varying Force-of-Infection (FoI) model.
prob_seroprev_by_age | Generate probabilities of seropositivity by age based on model choice.
prob_seroprev_gen_by_age | Generate probabilities of seropositivity by age based on a general Force-of-Infection (FoI) model.
prob_seroprev_time_by_age | Generate probabilities of seropositivity by age based on a time-varying Force-of-Infection (FoI) model.
serofoi | The 'serofoi' package.
set_foi_init | Sets initialization function for sampling
set_stan_data_defaults | Set stan data defaults for sampling
sf_cauchy | Sets Cauchy distribution parameters for sampling
sf_none | Sets empty prior distribution
sf_normal | Sets normal distribution parameters for sampling
sf_uniform | Sets uniform distribution parameters for sampling
simulate_serosurvey | Simulate serosurvey data based on various Force-of-Infection (FoI) models.
simulate_serosurvey_age | Simulate serosurvey data based on an age-varying Force-of-Infection (FoI) model.
simulate_serosurvey_age_time | Simulate serosurvey data based on an age-and-time-varying Force-of-Infection (FoI) model.
simulate_serosurvey_general | Simulate serosurvey data based on general serocatalytic model.
simulate_serosurvey_time | Simulate serosurvey data based on a time-varying Force-of-Infection (FoI) model.
summarise_central_estimate | Summarise central estimate
summarise_loo_estimate | Extract specified loo estimate
summarise_seromodel | Summarise specified model
veev2012 | Venezuelan Equine Encephalitis Virus (VEEV) seroprevalence data in serofoi