simulate_group: Simulate group data

In seroanalytics/serosolver: Inference Framework for Serological Data

Simulate group data

Description

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

Usage

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,
  DOBs = NULL
)

Arguments

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 example_antigenic_map
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
DOBs	vector giving the time period of birth (entries corresponding to 'strain_isolation_times')

Value

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

See Also

simulate_individual, simulate_individual_faster

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

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