simulate_individual_faster: Simulate individual data quickly

In seroanalytics/serosolver: Inference Framework for Serological Data

Simulate individual data quickly

Description

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.

Usage

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
)

Arguments

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 create_cross_reactivity_vector
antigenic_map_short	the short term antigenic cross reactivity map generated from create_cross_reactivity_vector
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

Value

a data frame with columns samples, virus and titre of simulated data

See Also

Other simulation_functions: simulate_attack_rates(), simulate_data(), simulate_group(), simulate_individual(), simulate_infection_histories()

seroanalytics/serosolver documentation built on April 24, 2023, 9:52 a.m.