R/model.R

In mrc-ide/gonovax: Deterministic Compartmental Model of Gonorrhoea with Vaccination

##' @name model
##' @title Model of gonorrhoea with dual vaccines
##'This is an odin model.
##' @export model
NULL



##' @name run
##' @title Run odin model of gonorrhoea with or without vaccination
##' @param tt a numeric vector of times at which the model state is output
##' @param gono_params a data frame of parameters
##' @param demographic_params A dataframe of demographic parameters
##' @param init_params A list of starting conditions
##' @param vax_params A vector of vaccination params
##' @param n_diag_rec integer for the number of diagnosis history substrata
##' @param transform = TRUE
##' @export run

run <- function(tt, gono_params, demographic_params = NULL,
                init_params = NULL, vax_params = NULL,
                n_diag_rec = 1, transform = TRUE) {

  pars <- model_params(gono_params = gono_params,
                       demographic_params = demographic_params,
                       init_params = init_params,
                       vax_params = vax_params,
                       n_diag_rec = n_diag_rec)
  mod <- model$new(user = pars, unused_user_action = FALSE)
  y <- mod$run(tt)

  if (transform) {
    y <- mod$transform_variables(y)
  }

  y
}

##' @name run_xpvwrh
##' @title Run odin model of gonorrhoea with or without vaccination
##' @param tt a numeric vector of times at which the model state is output
##' @param gono_params a data frame of parameters
##' @param demographic_params A dataframe of demographic parameters
##' @param init_params A list of starting conditions
##' @param vax_params A vector of vaccination params
##' @param n_erlang integer giving the number of transitions that need to be
##'  made through vaccine-protected strata until that protection has waned
##' @param n_diag_rec integer for the number of diagnosis history substrata
##' @param years_history number of years that diagnosis history is recorded for
##' @param transform = TRUE
##' @export run

run_xpvwrh <- function(tt, gono_params, demographic_params = NULL,
                       init_params = NULL, vax_params = NULL,
                       n_erlang = 1, n_diag_rec = 1, years_history = 1,
                       transform = TRUE) {

  pars <- model_params_xpvwrh(gono_params = gono_params,
                              demographic_params = demographic_params,
                              init_params = init_params,
                              vax_params = vax_params,
                              n_erlang = n_erlang,
                              n_diag_rec = n_diag_rec,
                              years_history = years_history)

  mod <- model$new(user = pars, unused_user_action = FALSE)
  y <- mod$run(tt)

  if (transform) {
    y <- mod$transform_variables(y)
  }

  y
}

##' @name run_xpvwrh_trackvt
##' @title Run odin model of gonorrhoea with or without vaccination
##' @param tt a numeric vector of times at which the model state is output
##' @param gono_params a data frame of parameters
##' @param demographic_params A dataframe of demographic parameters
##' @param init_params A list of starting conditions
##' @param vax_params A vector of vaccination params
##' @param n_erlang integer giving the number of transitions that need to be
##'  made through vaccine-protected strata until that protection has waned
##' @param n_diag_rec integer for the number of diagnosis history substrata
##' @param years_history number of years that diagnosis history is recorded for
##' @param transform = TRUE
##' @export run

run_xpvwrh_trackvt <- function(tt, gono_params, demographic_params = NULL,
                               init_params = NULL, vax_params = NULL,
                               n_erlang = 1, n_diag_rec = 1, years_history = 1,
                               transform = TRUE) {

  pars <- model_params_xpvwrh_trackvt(gono_params = gono_params,
                                      demographic_params = demographic_params,
                                      init_params = init_params,
                                      vax_params = vax_params,
                                      n_erlang = n_erlang,
                                      n_diag_rec = n_diag_rec,
                                      years_history = years_history)

  mod <- model$new(user = pars, unused_user_action = FALSE)
  y <- mod$run(tt)

  if (transform) {
    y <- mod$transform_variables(y)
  }

  y
}