R/09-ph_set_virus.R

In como-ph/comoparams: R Utility Tool to Extract, Process and Structure Philippines-Specific Datasets for Use in CoMo Consortium Model

################################################################################
#
#'
#' Set Philippines-specific CoMo model simulation parameters for virus
#' parameters
#'
#' @return A list of Philippines-specific CoMo model parameters for virus
#'   parameters
#'
#' @examples
#' ph_set_virus()
#'
#' @export
#'
#
################################################################################

ph_set_virus <- function() {
  ## Header
  cli::cli_h1(text = "Setting CoMo modeling VIRUS parameters for the Philippines\n")
  cat("\n")

  ## Check if session is interactive
  if(interactive()) {

    ## Confirm if ready to proceed
    set_params <- utils::menu(choices = c("Yes", "No"),
                              title = "Are you ready to proceed?")

    if(set_params == 1) {
      ## Input relative infectiousness of incubation phase
      cat("\n")
      cli::cli_h2("Relative infectiousness of incubation phase")
      cat("\n")
      cli::cli_h3("Current literature suggest a default value of 10%.")
      rho_default <- utils::menu(choices = c("Yes", "No"),
                                 title = "Should default value be used?")

      if(rho_default == 2) {
        repeat {
          ## Relative infectiousness of incubation phase
          rho <- readline(prompt = "Relative infectiousness of incubation phase (numeric; %): ")

          ## Check that rho is in correct format (numeric)
          if(is.na(rho) | rho == "") {
            cat("\n")
            cli::cli_alert_danger("{cli::col_red('Relative infectiousness of incubation phase should be provided. Try again.')}")
            cat("\n")
          } else {
            if(stringr::str_detect(string = rho, pattern = "[a-zA-Z]")) {
              cat("\n")
              cli::cli_alert_danger("{cli::col_red('Relative infectiousness of incubation phase should be numeric. Try again.')}")
              cat("\n")
            } else {
              if(as.numeric(rho) <= 0) {
                cat("\n")
                cli::cli_alert_danger("{cli::col_red('Relative infectiousness of incubation phase cannot be 0% or less. Try again.')}")
                cat("\n")
              }
              if(as.numeric(rho) > 100 ) {
                cat("\n")
                cli::cli_alert_danger("{cli::col_red('Relative infectiousness of incubation phase cannot be more than 100%. Try again.')}")
                cat("\n")
              }
            }
          }

          ## If in correct format, go to next
          if(stringr::str_detect(string = rho, pattern = "[0-9]")) {
            if(as.numeric(rho) > 0 &
              as.numeric(rho) <= 100) break
          }
        }
      } else rho <- 10

      ## Input average incubation period
      if(!is.null(rho) | !is.na(rho)) {
        cat("\n")
        cli::cli_h2("Average incubation period\n")
        cat("\n")
        cli::cli_h3("Current literature suggest a default value of 3.5 days. ")
        gamma_default <- utils::menu(choices = c("Yes", "No"),
                                     title = "Should default value be used?")
        cat("\n")

        if(gamma_default == 2) {
          repeat {
            ## Average incubation period
            gamma <- readline(prompt = "Average incubation period (numeric; days): ")

            ## Check that gamma is in correct format (numeric)
            if(is.na(gamma) | gamma == "") {
              cat("\n")
              cli::cli_alert_danger("{cli::col_red('Average incubation period should be provided. Try again.')}")
              cat("\n")
            } else {
              if(stringr::str_detect(string = gamma, pattern = "[a-zA-Z]")) {
                cat("\n")
                cli::cli_alert_danger("{cli::col_red('Average incubation period should be numeric. Try again.')}")
                cat("\n")
              } else {
                if(as.numeric(gamma) <= 0) {
                  cat("\n")
                  cli::cli_alert_danger("{cli::col_red('Average incubation period cannot be 0 or less. Try again.')}")
                  cat("\n")
                }
                if(as.numeric(gamma) > 7 ) {
                  cat("\n")
                  cli::cli_alert_danger("{cli::col_red('Average incubation period cannot be more than 7. Try again.')}")
                  cat("\n")
                }
              }
            }

            ## If in correct format, go to next
            if(stringr::str_detect(string = gamma, pattern = "[0-9]")) {
              if(as.numeric(gamma) > 0 &
                as.numeric(gamma) <= 7) break
            }
          }
        } else gamma <- 3.5
      }

      ## Input average duration of symptomatic infection period
      if(!is.null(gamma) | !is.na(gamma)) {
        cat("\n")
        cli::cli_h2("Average duration of symptomatic infection period")
        cat("\n")
        cli::cli_h3("Current literature suggest a default value of 4.5 days. ")
        nui_default <- utils::menu(choices = c("Yes", "No"),
                                   title = "Should default value be used?")
        cat("\n")

        if(nui_default == 2) {
          repeat {
            ## Average duration of symptomatic infection period
            nui <- readline(prompt = "Average duration of symptomatic infection period (numeric; days): ")

            ## Check that nui is in correct format (numeric)
            if(is.na(nui) | nui == "") {
              cat("\n")
              cli::cli_alert_danger("{cli::col_red('Average duration of symptomatic infection period should be provided. Try again.')}")
              cat("\n")
              } else {
                if(stringr::str_detect(string = nui, pattern = "[a-zA-Z]")) {
                  cat("\n")
                  cli::cli_alert_danger("{cli::col_red('Average duration of symptomatic infection period should be numeric. Try again.')}")
                  cat("\n")
                } else {
                  if(as.numeric(nui) <= 0) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Average duration of symptomatic infection period cannot be 0 or less. Try again.')}")
                    cat("\n")
                  }
                  if(as.numeric(nui) > 7 ) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Average duration of symptomatic infection period cannot be more than 7. Try again.')}")
                    cat("\n")
                  }
                }
              }

              ## If in correct format, go to next
              if(stringr::str_detect(string = nui, pattern = "[0-9]")) {
                if(as.numeric(nui) > 0 &
                  as.numeric(nui) <= 7) break
              }
            }
          } else nui <- 4.5
        }

        ## Input month of peak infectivity of the virus
        if(!is.null(nui) | !is.na(nui)) {
          cat("\n")
          cli::cli_h2("Month of peak infectivity of the virus\n")
          cat("\n")
          cli::cli_h3("Current literature suggest a default value of January (1).")
          phi_default <- utils::menu(choices = c("Yes", "No"),
                                     title = "Should default value be used?")
          cat("\n")

          if(phi_default == 2) {
            ## Average duration of symptomatic infection period
            phi <- utils::menu(choices = month.name,
                               title = "Month of peak infectivity of the virus")
          } else phi <- 1
        }

        ## Input annual variation in infectivity of the virus
        if(!is.null(phi) | !is.na(phi)) {
          cat("\n")
          cli::cli_h2("Annual variation in infectivity of the virus\n")
          cat("\n")
          cli::cli_h3("Current literature suggest a default value of 0%. ")
          amp_default <- utils::menu(choices = c("Yes", "No"),
                                     title = "Should default value be used?")
          cat("\n")

          if(amp_default == 2) {
            repeat {
              ## Annual variation in infectivity of the virus
              amp <- readline(prompt = "Annual variation in infectivity of the virus (numeric; %): ")

              ## Check that amp is in correct format (numeric)
              if(is.na(amp) | amp == "") {
                cat("\n")
                cli::cli_alert_danger("{cli::col_red('Annual variation in infectivity of the virus should be provided. Try again.')}")
                cat("\n")
              } else {
                if(stringr::str_detect(string = amp, pattern = "[a-zA-Z]")) {
                  cat("\n")
                  cli::cli_alert_danger("{cli::col_red('Annual variation in infectivity of the virus should be numeric. Try again.')}")
                  cat("\n")
                } else {
                  if(as.numeric(amp) < 0) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Annual variation in infectivity of the virus cannot be less than 0%. Try again.')}")
                    cat("\n")
                  }
                  if(as.numeric(amp) > 100 ) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Annual variation in infectivity of the virus cannot be more than 100%. Try again.')}")
                    cat("\n")
                  }
                }
              }

              ## If in correct format, go to next
              if(stringr::str_detect(string = amp, pattern = "[0-9]")) {
                if(as.numeric(amp) >= 0 &
                  as.numeric(amp) <= 100) break
              }
            }
          } else amp <- 0
        }

        ## Input average duration of immunity
        if(!is.null(amp) | !is.na(amp)) {
          cat("\n")
          cli::cli_h2("Average duration of immunity")
          cat("\n")
          cli::cli_h3("A default value of 150 years is suggested.")
          omega_default <- utils::menu(choices = c("Yes", "No"),
                                       title = "Should default value be used?")
          cat("\n")

          if(omega_default == 2) {
            repeat {
              ## Average duration of immunity
              omega <- readline(prompt = "Average duration of immunity (numeric; years): ")

              ## Check that omega is in correct format (numeric)
              if(is.na(omega) | omega == "") {
                cat("\n")
                cli::cli_alert_danger("{cli::col_red('Average duration of immunity should be provided. Try again.')}")
                cat("\n")
              } else {
                if(stringr::str_detect(string = omega, pattern = "[a-zA-Z]")) {
                  cat("\n")
                  cli::cli_alert_danger("{cli::col_red('Average duration of immunity should be numeric. Try again.')}")
                  cat("\n")
                } else {
                  if(as.numeric(omega) < 0.5) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Average duration of immunity cannot be less than 0.5. Try again.')}")
                    cat("\n")
                  }
                  if(as.numeric(omega) > 150 ) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Average duration of immunity cannot be more than 150. Try again.')}")
                    cat("\n")
                  }
                }
              }

              ## If in correct format, go to next
              if(stringr::str_detect(string = omega, pattern = "[0-9]")) {
                if(as.numeric(omega) >= 0.5 &
                  as.numeric(nui) <= 150) break
              }
            }
          } else omega <- 150
        }

        ## Input probability upon infection of developing clinical symptoms
        if(!is.null(omega) | !is.na(omega)) {
          cat("\n")
          cli::cli_h2("Probability upon infection of developing clinical symptoms")
          cat("\n")
          cli::cli_h3("Current literature suggest a default value of 55%. ")
          pclin_default <- utils::menu(choices = c("Yes", "No"),
                                       title = "Should default value be used?")
          cat("\n")

          if(pclin_default == 2) {
            repeat {
              ## Probability upon infection of developing clinical symptoms
              pclin <- readline(prompt = "Probability upon infection of developing clinical symptoms (numeric; %): ")

              ## Check that pclin is in correct format (numeric)
              if(is.na(pclin) | pclin == "") {
                cat("\n")
                cli::cli_alert_danger("{cli::col_red('Probability upon infection of developing clinical symptoms should be provided. Try again.')}")
                cat("\n")
              } else {
                if(stringr::str_detect(string = pclin, pattern = "[a-zA-Z]")) {
                  cat("\n")
                  cli::cli_alert_danger("{cli::col_red('Probability upon infection of developing clinical symptoms should be numeric. Try again.')}")
                  cat("\n")
                } else {
                  if(as.numeric(pclin) <= 0) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Probability upon infection of developing clinical symptoms cannot be 0% or less. Try again.')}")
                    cat("\n")
                  }
                  if(as.numeric(pclin) >= 100 ) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Probability upon infection of developing clinical symptoms cannot be 100% or more. Try again.')}")
                    cat("\n")
                  }
                }
              }

              ## If in correct format, go to next
              if(stringr::str_detect(string = pclin, pattern = "[0-9]")) {
                if(as.numeric(pclin) > 0 &
                  as.numeric(pclin) < 100) break
              }
            }
          } else pclin <- 55
        }

        ## Input probability upon hospitalisation of requiring ICU admission
        if(!is.null(pclin) | !is.na(pclin)) {
          cat("\n")
          cli::cli_h2("Probability upon hospitalisation of requiring ICU admission")
          cat("\n")
          cli::cli_h3("Current literature suggest a default value of 50%. ")
          prob_icu_default <- utils::menu(choices = c("Yes", "No"),
                                          title = "Should default value be used?")

          if(prob_icu_default == 2) {
            repeat {
              ## Probability upon hospitalisation of requiring ICU admission
              prob_icu <- readline(prompt = "Probability upon hospitalisation of requiring ICU admission (numeric; %): ")

              ## Check that prob_icu is in correct format (numeric)
              if(is.na(prob_icu) | prob_icu == "") {
                cat("\n")
                cli::cli_alert_danger("{cli::col_red('Probability upon hospitalisation of requiring ICU admission should be provided. Try again.')}")
                cat("\n")
              } else {
                if(stringr::str_detect(string = prob_icu, pattern = "[a-zA-Z]")) {
                  cat("\n")
                  cli::cli_alert_danger("{cli::col_red('Probability upon hospitalisation of requiring ICU admission should be numeric. Try again.')}")
                  cat("\n")
                } else {
                  if(as.numeric(prob_icu) <= 0) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Probability upon hospitalisation of requiring ICU admission cannot be 0% or less. Try again.')}")
                    cat("\n")
                  }
                  if(as.numeric(prob_icu) >= 100 ) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Probability upon hospitalisation of requiring ICU admission cannot be 100% or more. Try again.')}")
                    cat("\n")
                  }
                }
              }

              ## If in correct format, go to next
              if(stringr::str_detect(string = prob_icu, pattern = "[0-9]")) {
                if(as.numeric(prob_icu) > 0 &
                  as.numeric(prob_icu) < 100) break
              }
            }
          } else prob_icu <- 50
        }

        ## Input probability upon admission to the ICU of requiring a ventilator
        if(!is.null(prob_icu) | !is.na(prob_icu)) {
          cat("\n")
          cli::cli_h2("Probability upon admission to the ICU of requiring a ventilator\n")
          cat("\n")
          cli::cli_h3("Current literature suggest a default value of 75%. ")
          prob_vent_default <- utils::menu(choices = c("Yes", "No"),
                                           title = "Should default value be used?")

          if(prob_vent_default == 2) {
            repeat {
              ## Probability upon admission to the ICU of requiring a ventilator
              prob_vent <- readline(prompt = "Probability upon admission to the ICU of requiring a ventilator (numeric; %): ")

              ## Check that prob_vent is in correct format (numeric)
              if(is.na(prob_vent) | prob_vent == "") {
                cat("\n")
                cli::cli_alert_danger("{cli::col_red('Probability upon admission to the ICU of requiring a ventilator should be provided. Try again.')}")
                cat("\n")
              } else {
                if(stringr::str_detect(string = prob_vent, pattern = "[a-zA-Z]")) {
                  cat("\n")
                  cli::cli_alert_danger("{cli::col_red('Probability upon admission to the ICU of requiring a ventilator should be numeric. Try again.')}")
                  cat("\n")
                } else {
                  if(as.numeric(prob_vent) <= 0) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Probability upon admission to the ICU of requiring a ventilator cannot be 0% or less. Try again.')}")
                    cat("\n")
                  }
                  if(as.numeric(prob_vent) >= 100 ) {
                    cat("\n")
                    cli::cli_alert_danger("{cli::col_red('Probability upon admission to the ICU of requiring a ventilator cannot be 100% or more. Try again.')}")
                    cat("\n")
                  }
                }
              }

              ## If in correct format, go to next
              if(stringr::str_detect(string = prob_vent, pattern = "[0-9]")) {
                if(as.numeric(prob_vent) > 0 &
                  as.numeric(prob_vent) < 100) break
              }
            }
          } else prob_vent <- 75
        }
      } else {
        ##
        rho       <- NA
        gamma     <- NA
        nui       <- NA
        phi       <- NA
        amp       <- NA
        omega     <- NA
        pclin     <- NA
        prob_icu  <- NA
        prob_vent <- NA

        ##
        cat("\n")
        cli_alert_warning("{cli::col_red('VIRUS parameters have NOT been set.')}")
        cat("\n")
      }

    if(all(!is.na(c(rho, gamma, nui, phi, amp, omega,
                    pclin, prob_icu, prob_vent)))) {
      ##
      cat("\n")
      cli::cli_text(text = "{cli::col_green(cli::symbol$tick)}
                            {cli::col_green('VIRUS parameters have been set.')} |
                            {cli::col_blue(cli::symbol$arrow_right)}
                            {cli::col_blue('Proceed to next parameter.')}")
      cat("\n")
    }
  } else {
    cat("\n")
    cli::cli_alert_danger(text = "{cli::col_red('VIRUS parameters have NOT been set.')}")
    cli::cli_text(text = "{cli::col_red('Setting VIRUS modelling parameters require interactive input from user. Try again.)}")

    ##
    rho       <- NA
    gamma     <- NA
    nui       <- NA
    phi       <- NA
    amp       <- NA
    omega     <- NA
    pclin     <- NA
    prob_icu  <- NA
    prob_vent <- NA
  }

  ## Concatenate params
  params <- list(as.numeric(rho), as.numeric(gamma), as.numeric(nui),
                 as.numeric(phi), as.numeric(amp), as.numeric(omega),
                 as.numeric(pclin), as.numeric(prob_icu),
                 as.numeric(prob_vent))

  names(params) <- c("rho", "gamma", "nui", "phi", "amp", "omega",
                     "pclin", "prob_icu", "prob_vent")

  ## Return params
  return(params)
}