Package index • serosolver

Fit and simulate models
`serosolver()`	Run the serosolver model
`simulate_data()`	Simulate full data set
`simulate_attack_rates()`	Simulate attack rates
`simulate_infection_histories()`	Simulate infection histories
`simulate_antibody_model()`	Simulate the antibody model
Prepare and check inputs
`check_data()`	Checks the entries of data used in serosolver
`check_demographics()`	Checks the entries of demographics data frame used for parameter stratification
`check_inf_hist()`	Check infection history matrix
`check_par_tab()`	Check and prepare a model parameter table
`check_attack_rates()`	Checks the attack_rates supplied in simulate_data
`generate_antigenic_map_flexible()`	Generate antigenic map, flexible
`load_antibody_data()`	Load serological antibody data from CSV file
`load_antigenic_map()`	Load in antigenic map file from CSV
`create_age_mask()`	Create age mask
`create_sample_mask()`	Create sample mask
Model options and priors
`create_start_level_data()`	Generate starting antibody levels
`add_rhos_par_tab()`	Add measurement offset values to par_tab
`extend_par_tab_biomarker_groups()`	Extend parameter table for multiple biomarker_groups
`generate_start_tab()`	Generate starting parameter table
`describe_priors()`	Describe infection history priors
`find_beta_prior_mode()`	Find Beta distribution parameters with mode
`find_beta_prior_with_mean()`	Find beta parameters with maximum variance
`find_beta_prior_with_mean_var()`	Find beta parameters for mean and variance
MCMC output and summaries
`load_start_tab()`	Load a starting parameter table from file
`load_theta_chains()`	Load MCMC chains from CSV files for antibody kinetics parameters (theta)
`load_infection_chains()`	Load MCMC chains from CSV files for infection histories
`load_mcmc_chains()`	Load MCMC chains for the antibody kinetics parameters and infection histories from CSV outputs
`get_antibody_level_predictions()`	Generate antibody level credible intervals
`calculate_infection_history_statistics()`	Get posterior information for estimated infection histories
`get_best_pars()`	Best pars
`get_best_draw()`	Best infection history and theta parameters
`get_index_pars()`	Index pars
`pad_inf_chain()`	Pad infection history chain
`get_n_alive()`	Get number alive
`get_n_alive_group()`	Get number alive by population group
`get_total_number_infections()`	Get total number of infections
`generate_quantiles()`	Formatted quantiles
`identify_run_lengths()`	Identify runs of infections from posterior
`summarize_run_lengths()`	Summarize runs of infections from posterior
Plotting and diagnostics
`plot_2d_density()`	Plot joint posterior densities for two parameters
`plot_antibody_data()`	Plot raw data
`plot_antibody_dependent_boosting()`	Antibody dependent boosting relationship
`plot_antibody_model()`	Plot the antibody model
`plot_antibody_predictions()`	Plots model predicted titers against observations
`plot_attack_rates()`	Plot historical attack rates with pointrange plots
`plot_cumulative_infection_histories()`	Plot cumulative and per time posterior infection probability densities
`plot_estimated_antibody_model()`	Plots estimated antibody kinetics model
`plot_individual_number_infections()`	Plot point range number infections per individual
`plot_infection_history_chains_indiv()`	Plot MCMC trace for infections per individual
`plot_infection_history_chains_time()`	Plot MCMC trace for infections per year
`plot_infection_history_posteriors()`	Plot inferred posteriors infection histories
`plot_mcmc_diagnostics()`	Plot MCMC diagnostics
`plot_model_fits()`	Plots infection histories and antibody model
`plot_posteriors_theta()`	Plot posterior parameter traces and densities
`plot_samples_distances()`	Plot time between serum samples
`plot_total_number_infections()`	Total number of infections
Example data
`example_antibody_data`	Example antibody data
`example_longitudinal_antibody_data`	Example longitudinal antibody data
`example_multiple_biomarker_groups_data`	Example antibody data with multiple biomarker groups
`example_antigenic_map`	Example antigenic map
`example_inf_chain`	Example MCMC chain for infection histories
`example_inf_hist`	Example infection history matrix
`example_par_tab`	Example parameter table
`example_theta_chain`	Example MCMC chain for kinetics parameters

Reference

Fit and simulate models

Prepare and check inputs

Model options and priors

MCMC output and summaries

Plotting and diagnostics

Example data