Man pages for serofoi
Bayesian Estimation of the Force of Infection from Serological Data
| 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 |
| check_age_constraints | Check min and max age consistency for validation purposes |
| chik2015 | Chikungunya seroprevalence data in serofoi |
| extract_central_estimates | Extracts central estimates from stan_fit object for specified... |
| fit_seromodel | Runs specified stan model for the Force-of-Infection (FoI) |
| get_foi_index | Generates Force-of-Infection indexes for heterogeneous age... |
| get_seroprev_counts_by_bin | Generate seropositivity counts by bin given the probability... |
| 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... |
| probability_exact_time_varying | Computes the probability of being seropositive when... |
| prob_seroprev_age_by_age | Generate probabilities of seropositivity by age based on an... |
| prob_seroprev_age_time_by_age | Generate probabilities of seropositivity by age based on an... |
| prob_seroprev_by_age | Generate probabilities of seropositivity by age based on... |
| prob_seroprev_gen_by_age | Generate probabilities of seropositivity by age based on a... |
| prob_seroprev_time_by_age | Generate probabilities of seropositivity by age based on a... |
| serofoi-package | 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... |
| simulate_serosurvey_age | Simulate serosurvey data based on an age-varying... |
| simulate_serosurvey_age_time | Simulate serosurvey data based on an age-and-time-varying... |
| simulate_serosurvey_general | Simulate serosurvey data based on general serocatalytic... |
| simulate_serosurvey_time | Simulate serosurvey data based on a time-varying... |
| summarise_central_estimate | Summarise central estimate |
| summarise_loo_estimate | Extract specified loo estimate |
| summarise_seromodel | Summarise specified model |
| validate_foi_df | Helper function to validate FoI structure for simulation |
| validate_foi_index | Helper function to validate FoI index consistency |
| validate_plot_constant | Helper function to validate whether the current plot... |
| validate_seroreversion_rate | Helper function to validate seroreversion rate properties for... |
| validate_serosurvey | Helper function to validate serosurvey structure |
| validate_simulation_age | Helper function to validate consistency between the FoI and... |
| validate_simulation_age_time | Helper function to validate consistency between the FoI and... |
| validate_survey_features | Helper function to validate serosurvey features for... |
| veev2012 | Venezuelan Equine Encephalitis Virus (VEEV) seroprevalence... |
