Bayesian Estimation of the Force of Infection from Serological Data

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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