simulate_individual: Simulate individual data

In adamkucharski/serosolver: Inference Framework for Serological Data

Simulate individual data

Description

Simulates a full set of antibody data for an individual with known theta and infection_history.

Usage

simulate_individual(
  theta,
  infection_history,
  antigenic_map,
  sampling_times,
  possible_exposure_times,
  measured_biomarker_ids,
  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	(optional) A data frame of antigenic x and y coordinates. Must have column names: x_coord; y_coord; inf_times. See example_antigenic_map.
sampling_times	vector of times at which blood samples were taken
possible_exposure_times	(optional) If no antigenic map is specified, this argument gives the vector of times at which individuals can be infected
measured_biomarker_ids	vector of which biomarker IDs had measurements in 'possible_exposure_times'
measurement_indices	default NULL, optional vector giving the index of ‘measurement_bias' that each antigen/biomarker ID 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)
repeats	number of repeat observations for each year

Value

a data frame with columns samples, biomarker IDs and antibody levels of simulated data

See Also

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

Examples

data(example_par_tab)
data(example_antigenic_map)
infection_history <- sample(c(0,1),size=nrow(example_antigenic_map), replace=TRUE,prob=c(0.9,0.1))
pars <- example_par_tab$values
names(pars) <- example_par_tab$names
possible_exposure_times <- example_antigenic_map$inf_times
y <- simulate_individual(pars, infection_history, example_antigenic_map, 2009, 
                         possible_exposure_times,possible_exposure_times,add_noise=FALSE)

adamkucharski/serosolver documentation built on April 28, 2024, 6:19 p.m.