| add_measurement_shifts | Add measurement shifts to predictions |
| add_noise | Add noise |
| bb_mean | Beta binomial mean |
| bb_var | Beta binomial variance |
| calc_phi_probs | Calculate FOI log probability |
| calc_phi_probs_indiv | Calculate FOI log probability vector |
| calc_phi_probs_spline | Calculate FOI from spline - INACTIVE |
| calculate_infection_history_statistics | Get posterior information infection histories |
| check_attack_rates | Checks the attack_rates supplied in simulate_data |
| check_data | Checks the entries of data used in run_MCMC |
| check_inf_hist | Check infection history matrix |
| check_par_tab | Check par_tab for simulate_data |
| check_proposals | Checks if the multivariate proposal is being used with the... |
| create_age_mask | Create age mask |
| create_cross_reactivity_vector | Convert melted antigenic map to cross reactivity |
| create_posterior_func | Posterior function pointer |
| create_prior_mu | Create strain specific bias prior |
| create_prob_shifts | Measurement shift creation |
| create_strain_mask | Create strain mask |
| cs1_chains_real | MCMC chains case study 1, real |
| cs1_chains_real_b | MCMC chains case study 1, real, for sim |
| cs1_chains_sim | MCMC chains case study 1, sim |
| cs2_chains_real | MCMC chains case study 2, real |
| cs2_chains_real_b | MCMC chains case study 2, real, for sim |
| cs2_chains_sim | MCMC chains case study 2, sim |
| db | Beta prior on an infection |
| dbb | Beta binomial density |
| dbb_prior | Beta binomial prior used here (no choose constant) |
| density_beta_binom | Beta binomial density |
| describe_priors | Describe infection history priors |
| estimate_mode | Estimate vector mode |
| 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 |
| example_titre_dat | Example titre data |
| expand_summary_inf_chain | Expands default MCMC saved inf_chain |
| expand_summary_infChain | Expand sparse infection history matrix |
| Fast-observation-error-function-continuous | Fast observation error function continuous Calculate the... |
| find_bb_2 | Beta binomial parameter match |
| 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 |
| find_prior_alpha_beta | Beta binomial parameters |
| fit_beta_prior | Fit beta distribution to MCMC output |
| fit_normal_prior | Fit normal distribution to MCMC output |
| fromUnitScale | Convert from unit scale to original scale |
| generate_antigenic_map | Generate antigenic map |
| generate_antigenic_map_flexible | Generate antigenic map, flexible |
| generate_ar_annual | Generates attack rates from an SIR model with fixed... |
| generate_cumulative_inf_plots | Plot cumulative and per time posterior infection probability... |
| generate_phis | Generate FOI phis - INACTIVE |
| generate_quantiles | Formatted quantiles |
| generate_start_tab | Generate starting parameter table |
| gen_spline_y | Generates a spline for 'generate_phis' - INACTIVE |
| get_best_pars | Best pars |
| get_DOBs | Get DOBs |
| get_index_pars | Index pars |
| get_n_alive | Get number alive |
| get_n_alive_group | Get number alive by location |
| get_titre_predictions | Generate titre credible intervals |
| get_total_number_infections | Get total number of infections |
| hist_rbb | Beta binomial histogram |
| infection_history_prior | Beta binomial infection history prior |
| infection_history_symmetric | Brute force infection history proposal |
| inf_hist_prop_prior_v2_and_v4 | Infection history gibbs proposal |
| inf_hist_prop_prior_v3 | Fast infection history proposal function |
| inf_hist_swap | Swap infection history years |
| inf_hist_swap_phi | Swap infection history years with phi term |
| inf_mat_prior | Infection history prior R |
| inf_mat_prior_cpp | Marginal prior probability (p(Z)) of a particular infection... |
| inf_mat_prior_cpp_vector | Marginal prior probability (p(Z)) of a particular infection... |
| inf_mat_prior_group_cpp | Marginal prior probability (p(Z)) of infection history matrix... |
| inf_mat_prior_group_cpp_vector | Marginal prior probability (p(Z)) of a particular infection... |
| inf_mat_prior_total_group_cpp | Marginal prior probability (p(Z)) of a particular infection... |
| likelihood_func_fast | Fast observation error function Calculate the probability of... |
| load_antigenic_map_file | Read in antigenic_map |
| load_infection_chains | Load MCMC chains for infection histories |
| load_mcmc_chains | Combine theta and infection history chains |
| load_start_tab | Read in start_tab |
| load_theta_chains | Load MCMC chains for theta |
| load_titre_dat | Read in titre_dat |
| melt_antigenic_coords | Create useable antigenic map |
| mvr_proposal | Multivariate proposal function |
| pad_alphas_and_betas | Pad par_tab with alpha and betas |
| pad_inf_chain | Pad infection history chain |
| pbb | Beta binomial distribution function |
| plot_attack_rates | Plot historical attack rates |
| plot_attack_rates_monthly | Plot historical attack rates monthly |
| plot_data | Useful plot for looking at simulated data |
| plot_infection_histories | Plots infection histories and titre model fits |
| plot_infection_histories_long | Plots infection histories and titre model fits longitudinal |
| 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_number_infections | Plot point range number infections per individual |
| plot_posteriors_infhist | Plot inferred posteriors infection histories |
| plot_posteriors_theta | Plot inferred posteriors theta |
| plot_samples_distances | Plot time between serum samples |
| plot_total_number_infections | Total number of infections |
| prob_mus | Prior probability of strain specific boosting |
| prob_shifts | Prior on measurement shifts |
| protect | Protect function |
| qbb | Beta binomial quantile function |
| rbb | Beta binomial random generation |
| r_likelihood | Likelihood function given discrete data (normal) |
| r_likelihood_continuous | Likelihood function given continuous data (normal) |
| rm_scale | Robins and Monro scaler, thanks to Michael White |
| run_MCMC | Adaptive Metropolis-within-Gibbs/Metropolis Hastings Random... |
| save_infection_history_to_disk | Write given infection history to disk |
| scaletuning | Scale step sizes |
| setup_infection_histories | Propose initial infection histories |
| setup_infection_histories_old | Propose initial infection histories - OLD VERSION |
| setup_infection_histories_titre | Propose initial infection histories based on titres - use... |
| setup_infection_histories_total | Initial infection history prior on total |
| setup_titredat_for_posterior_func | Setup titre data indices |
| simulate_attack_rates | Simulate attack rates |
| simulate_cross_sectional | Simulates multiple cohorts in a cross-sectional framework. |
| simulate_data | Simulate full data set |
| simulate_group | Simulate group data |
| simulate_individual | Simulate individual data |
| simulate_individual_faster | Simulate individual data quickly |
| simulate_infection_histories | Simulate infection histories |
| subset_nullable_vector | Takes a subset of a Nullable NumericVector, but only if it... |
| sum_buckets | Sums a vector based on bucket sizes |
| sum_infections_by_group | Count infections by group and time |
| sum_likelihoods | Sum likelihoods into buckets |
| titre_data_fast | Overall model function, fast implementation |
| titre_dependent_boosting_plot | Titre dependent boosting relationship |
| to.pdf | PDF - Rich's function to print to device without potential... |
| to.png | PNG - Rich's function to print to device without potential... |
| to.svg | SVG - Rich's function to print to device without potential... |
| toUnitScale | Convert to unit scale |
| univ_proposal | MCMC proposal function |
| wane_function | Function to calculate non-linear waning All additional... |
