run_forward_simulations: Run forward simulations

In mirjamlaager/mrsamcmc: An Implementation of Data Augmented MCMC for Inference on MRSA Transmission

Description

Run forward simulations

Usage

run_forward_simulations(data, baseline_parameters,
  intervention_parameters = NULL, n_iter, seed = NULL)

Arguments

data	a list containing 4 elements: patients a dataframe with three columns. Each row corresponds to a patient, the columns are admission, first_positive_test and discharge. Entries are in days. If there is no positive test for a patient, first_positive_test equals 20000. test_results_positive a matrix. Each row corresponds to a patient. Entries correspond to the day of a positive test. test_results_negative a matrix. Each row corresponds to a patient. Entries correspond to the day of a negative test. antibiotics a matrix. Each row corresponds to a patient. Entries correspond to the day when an antibiotic was administered.
baseline_parameters	a dataframe with values of all the parameters of the transmission model: beta the transmission rate b the effect of antibiotics on transmissibility s the effect of antibiotics on susceptibility rho_1 the test sensitivity in the absence of antibiotics rho_2 the test sensitivity in the presence of antibiotics phi the importation probability
intervention_parameters	a dataframe with the intervention settings: modfiy_transmission if FALSE (default), transmission is not modified and the baseline value of beta is used. If set to a value, the transmission rate is the baseline transmission rate multiplied by the value. decolonisation if TRUE, detected patients are decolonised. isolation if TRUE, detected patients are isolated.
n_iter	the number of forward simulations.
seed	set a seed for reproducibility of the simulations.

Value

The function returns a list with three elements:

positive_tests

the number of positive tests in each simulation.

negative_tests

the number of negative tests in each simulation.

parameter_samples

the random samples from the chains that were used for the simulations.

mirjamlaager/mrsamcmc documentation built on May 20, 2020, 11:13 a.m.