FOR USERS: USE simulate_individual. This function does the same thing, but with a few short cuts for speed. Simulates a full set of titre data for an individual with known theta and infection_history.
simulate_individual_faster( theta, infection_history, antigenic_map_long, antigenic_map_short, antigenic_distances, sampling_times, strain_isolation_times, measured_strains, mus = NULL, mu_indices = NULL, measurement_bias = NULL, measurement_indices = NULL, add_noise = TRUE, repeats = 1, DOB = NULL )
| theta | the named parameter vector |
|---|---|
| infection_history | the vector of 1s and 0s giving presence/absence of infections |
| antigenic_map_long | the long term antigenic cross reactivity map generated from |
| antigenic_map_short | the short term antigenic cross reactivity map generated from |
| antigenic_distances | same dimensions as antigenic_map_long and antigenic_map_short, but gives the raw euclidean antigenic distances |
| sampling_times | vector of times at which blood samples were taken |
| strain_isolation_times | (optional) If no antigenic map is specified, this argument gives the vector of times at which individuals can be infected |
| measured_strains | vector of which strains had titres measured in `strain_isolation_times` |
| mus | default NULL, optional vector of boosting parameters for each strain |
| mu_indices | default NULL, optional vector giving the index of `mus` that each strain uses the boosting parameter from. eg. if there are 6 circulation years in strain_isolation_times and 3 strain clusters, then this might be c(1,1,2,2,3,3) |
| measurement_indices | default NULL, optional vector giving the index of `measurement_bias` that each strain uses the measurement shift from from. eg. if there's 6 circulation years and 3 strain clusters, then this might be c(1,1,2,2,3,3) |
| add_noise | if TRUE, adds observation noise to the simulated titres |
| repeats | number of repeat observations for each year |
a data frame with columns samples, virus and titre of simulated data
Other simulation_functions:
simulate_attack_rates(),
simulate_data(),
simulate_group(),
simulate_individual(),
simulate_infection_histories()