parameter-settings.R

#' The Parameter Settings for the Methods and the Simulations

#' For debugging. Only a limited number of parameter settings is used, see 
#' parameter-settings.R. Only 
test_run <- FALSE

#' Parameter settings for the algorithms ------------------
algo_param <- data.frame(
  expand.grid(
))

#' Parameter settings for the simulation study ------------

if (test_run) { # simplify the parameters for a test run - this is debugging
  
  only_sim_param <- dplyr::as_tibble(
    expand.grid(
      n_patients = c(20),
      simulation_time = c(10),  
      prob_exposed = c(0.01), 
      avg_duration = c(5), 
      min_chance = c(1e-5), 
      max_chance = c(.1)
    )
  )
  
  risk_models <- dplyr::tibble(
    risk_model = c(
      'no-association',
      'current-use',
      'past-use',
      'withdrawal',
      'delayed',
      'decaying',
      'delayed+decaying',
      'long-term'
    )
  )
  
  sim_param <- merge(risk_models, only_sim_param)
  
  #' Parameters of the different risk models -----------------------------------
  
  #' no association ---------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "no-assocation"
    ))
  
  sim_method_all <-  sim_method
  
  #' current use ---------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "current-use"
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' past use ---------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "past-use", 
      past = c(5, 10)
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' withdrawal ---------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "withdrawal", 
      rate = c(.5, 1)
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' delayed ---------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "delayed", 
      mu = c(2, 5), 
      sigma = c(2)
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' decaying ---------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "decaying", 
      rate = c(.5, 1)
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' delayed + decaying ---------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "delayed+decaying", 
      mu = c(10), 
      sigma = c(2), 
      rate = c(.5)
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' long term ---------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "long-term", 
      rate = c(.25), 
      delay = c(50)
    ))
  
  sim_method_all <- dplyr::full_join(sim_method_all, sim_method)
  
  #' Combine all parameters for the simulations and the methods
  sim_param <- suppressWarnings(dplyr::left_join(sim_param, sim_method_all))
  
  #' provide a specific id to each parameter setting. This makes it 
  #' easier to process the results later on when there are repetitions
  sim_param$sim_param_id <- 1:nrow(sim_param)
  
} else { 
  
################################################################################
# PARAMETER SETTINGS FULL STUDY
################################################################################
  
  only_sim_param <- dplyr::as_tibble(
    expand.grid(
      n_patients = c(1000),
      simulation_time = c(100),  
      prob_exposed = c(0.01, 0.1,.5), 
      avg_duration = c(5), 
      min_chance = c(1e-4, 1e-3), 
      max_chance = c(.01,.1,.2,.3)
    )
  )
  
  # only_sim_param <- dplyr::tibble(
  #     n_patients = c(1000),
  #     simulation_time = c(100),  
  #     prob_exposed = c(0.05, 0.05, 0.05, 0.01, 0.01, 0.1, 0.1, 0.5), 
  #     avg_duration = c(5), 
  #     min_chance = c(1e-3, 5*1e-4, 1e-4, 5*1e-4, 1e-3, 5*1e-4, 1e-3, 1e-3), 
  #     max_chance = c(.3, .01, 0.01, 0.01, .3, 0.01, .3, .3)
  # )
  
  risk_models <- dplyr::tibble(
    risk_model = c(
      'no-association',
      'current-use',
      'past-use',
      'withdrawal',
      'delayed',
      'decaying',
      'delayed+decaying',
      'long-term'
    )
  )
  
  sim_param <- merge(risk_models, only_sim_param)
  
  #' Parameters of the different risk models -----------------------------------
  
  #' no association ---------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "no-assocation"
    ))
  
  sim_method_all <-  sim_method
  
  #' current use ---------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "current-use"
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' past use ---------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "past-use", 
      past = c(5, 10)
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' withdrawal --------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "withdrawal", 
      rate = c(.5, 1)
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' delayed --------------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "delayed", 
      mu = c(2, 5), 
      sigma = c(2)
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' decaying -----------------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "decaying", 
      rate = c(.5, 1)
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' delayed + decaying --------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "delayed+decaying", 
      mu = c(10), 
      sigma = c(2), 
      rate = c(.5)
    ))
  
  sim_method_all <-  dplyr::full_join(sim_method_all, sim_method)
  
  #' long term -----------------------
  sim_method <- dplyr::as_tibble(
    expand.grid(
      risk_model = "long-term", 
      rate = c(.25), 
      delay = c(50)
    ))
  
  sim_method_all <- dplyr::full_join(sim_method_all, sim_method)
  
  #' Combine all parameters for the simulations and the methods
  sim_param <- suppressWarnings(dplyr::left_join(sim_param, sim_method_all))
  
  #' provide a specific id to each parameter setting. This makes it 
  #' easier to process the results later on when there are repetitions
  sim_param$sim_param_id <- 1:nrow(sim_param)
}