Simulates a full set of titre data for n_indiv individuals with known theta and infection_histories. Each individual gets nsamps random samples from sampleTimes, and infections can occur at any of strain_isolation_times
simulate_group( n_indiv, theta, infection_histories, strain_isolation_times, measured_strains, sample_times, nsamps, antigenic_map, repeats = 1, mus = NULL, mu_indices = NULL, measurement_bias = NULL, measurement_indices = NULL, add_noise = TRUE )
| n_indiv | number of individuals to simulate |
|---|---|
| theta | the named parameter vector |
| infection_histories | the matrix of 1s and 0s giving presence/absence of infections for each individual |
| 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 strains that have titres measured matching entries in strain_isolation_times |
| nsamps | the number of samples each individual has (eg. nsamps=2 gives each individual 2 random sampling times from sampling_times) |
| antigenic_map | (optional) A data frame of antigenic x and y coordinates. Must have column names: x_coord; y_coord; inf_times. See |
| repeats | number of repeat observations for each year |
| 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 |
a data frame with columns individual, samples, virus and titre of simulated data
simulate_individual, simulate_individual_faster
Other simulation_functions:
simulate_attack_rates(),
simulate_data(),
simulate_individual_faster(),
simulate_individual(),
simulate_infection_histories()