cohort.RdRun stochastic individual model across trial cohort individuals in one or more clusters (alternate version incorporating more details of testing and reactive treatment during trial, in progress)
cohort( mainpop_data = list(), cluster_data = list(), n_patients = 1, prop_T_c = 0.9, age_start = 0.5, age_end = 10, flag_output = 0, test_time_values = c(), test_type = "clin", flag_pre_clearing = 1, censor_period = 0, flag_reactive_treatment = 1 )
| mainpop_data | List output by mainpop() containing main population data |
|---|---|
| cluster_data | List output by clusters_create() containing cluster data |
| n_patients | Number of trial cohort patients per cluster |
| prop_T_c | Treatment probability in cohort |
| age_start | Minimum age of trial cohort patients |
| age_end | Maximum age of trial cohort patients |
| flag_output | Integer indicating whether to show progress of simulation |
| test_time_values | Time points at which tests are administered |
| test_type | Type of test administered ("clin" = clinical, "RDT" = rapid diagnostic test) |
| flag_pre_clearing | Integer indicating whether patients given pre-trial prophylaxis (if 1, place all patients into prophylaxis category at start) |
| censor_period | Time period after a positive test during which a patient is not counted towards incidence |
| flag_reactive_treatment | Integer indicating whether patients are automatically given prophylaxis after a positive test (shifting them into treatment category if a clinical case, prophylaxis category otherwise) |
Takes a list of parameters, returns a list of raw data (data also saved to files as backup).