Package index • serofoi

All functions

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

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.

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

serofoi-package 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