Package index • serofoi

All functions

add_age_bins(): Add bins based on age intervals.

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

generate_random_sample_sizes(): Generate random sample sizes for each age group.

get_age_intervals(): Construct age-group variable from age column

get_foi_index(): Generates force-of-infection indexes for heterogeneous age groups

multinomial_sampling_group(): Generate random sample sizes using multinomial sampling.

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_seroprevalence_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_plotting(): Prepares serosurvey for plotting

probability_exact_age_varying(): Computes the probability of being seropositive when FOIs vary by age

probability_exact_time_varying(): Computes the probability of being seropositive when FOIs vary by time

probability_seropositive_age_and_time_model_by_age(): Generate probabilities of seropositivity by age based on an age-and-time varying FOI model.

probability_seropositive_age_model_by_age(): Generate probabilities of seropositivity by age based on an age-varying FOI model.

probability_seropositive_by_age(): Generate probabilities of seropositivity by age based user's choice of model.

probability_seropositive_general_model_by_age(): Generate probabilities of seropositivity by age based on a general FOI model.

probability_seropositive_time_model_by_age(): Generate probabilities of seropositivity by age based on a time-varying FOI model.

sample_size_by_individual_age_random(): Generate random sample sizes for each individual age based on survey features.

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 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 FOI models.

simulate_serosurvey_age_and_time_model(): Simulate serosurvey data based on an age-and-time-varying FOI model.

simulate_serosurvey_age_model(): Simulate serosurvey data based on an age-varying FOI model.

simulate_serosurvey_general_model(): Simulate serosurvey data based on general serocatalytic model.

simulate_serosurvey_time_model(): Simulate serosurvey data based on a time-varying FOI model.

summarise_central_estimate(): Summarise central estimate

summarise_loo_estimate(): Extract specified loo estimate

summarise_seromodel(): Summarise specified model

survey_by_individual_age(): Create a survey dataframe with per individual age information.

veev2012: Venezuelan Equine Encephalitis Virus (VEEV) seroprevalence data in serofoi