inst/virtual_patient_simulator/bs4/patient_generator.R

In CaPO4Sim: A Virtual Patient Simulator in the Context of Calcium and Phosphate Homeostasis

# Function needed to generate patients in the /www/datas folder


# id: patient id, must be unique
# name: patient name
# picture: path to image if any
# age: patient age
# height: patient height in cm
# weight: patient weight in kg
# gender: whether the patient is a male or female. Use to generate rendom avatar images
# medical_history -> list containing the following fields pathologies,
# examination_dates, doctors, doctors_gender, disease_description, disease_image that are also lists
# disease_id <- php1, hypopara, hypoD3, ... To set up the initial conditions

patient_generator <- function(id, name, picture = NULL, age, height, weight, gender,
                              pathologies = list() , examination_dates = list(),
                              doctors = list(), doctors_gender = list(),
                              disease_description = list(), disease_image = list(),
                              disease_id) {

  # raw folder
  raw_folder <- paste0(getwd(), "/www/")

  # check if the provided id is already used
  data_folder <- paste0(raw_folder, "patients_datas")
  file_list <- list.files(data_folder)
  n_patients <- length(file_list)

  if (n_patients > 0) {
    test <- lapply(1:n_patients, FUN = function(i) {
      temp <- readRDS(file = paste0(data_folder, "/", "patient_", i, ".rds"))
      if (id == temp$id) stop("You must choose a unique id number")
    })
  }

  # setup initial conditions depending on the disease_id
  state_folder <- paste0(raw_folder, "model_engine")
  if (disease_id == "php1") {
    state <- read.csv(paste0(state_folder, "/init_php1.csv"), stringsAsFactors = FALSE)
    state <- unlist(state[,-1])
  } else if (disease_id == "hypopara") {
    state <- read.csv(paste0(state_folder, "/init_hypopara.csv"), stringsAsFactors = FALSE)
    state <- unlist(state[,-1])
  } else if (disease_id == "hypoD3") {
    state <- read.csv(paste0(state_folder, "/init_hypoD3.csv"), stringsAsFactors = FALSE)
    state <- unlist(state[,-1])
  } else if (disease_id == "hyperD3") {
    state <- read.csv(paste0(state_folder, "/init_hyperD3.csv"), stringsAsFactors = FALSE)
    state <- unlist(state[,-1])
  }

  # set up random patient image
  patient_images_folder <- paste0(raw_folder, "patients_img")
  if (gender == "male") {
    patient_images_folder <- paste0(patient_images_folder, "/male")
  } else {
    patient_images_folder <- paste0(patient_images_folder, "/female")
  }
  random_image_number <- sample(1:12, 1)
  patient_avatar <- paste0(
    patient_images_folder,
    "/",
    list.files(patient_images_folder)[[random_image_number]]
  )
  patient_avatar <- unlist(str_split(string = patient_avatar, pattern = "www/"))[2]

  # set up a rendom doctor image
  doctor_images_folder <- paste0(raw_folder, "doctors_img")
  doctors_avatars <- lapply(1:length(doctors), FUN = function(i){
    if (doctors_gender[[i]] == "male") {
      doctor_images_folder <- paste0(doctor_images_folder, "/male")
    } else {
      doctor_images_folder <- paste0(doctor_images_folder, "/female")
    }
    random_image_number <- sample(1:7, 1)
    doctor_avatar <- paste0(
      doctor_images_folder,
      "/",
      list.files(doctor_images_folder)[[random_image_number]]
    )
    doctor_avatar <- unlist(str_split(string = doctor_avatar, pattern = "www/"))[2]
  })


  # if the previous id test id passed, generated the patient
  patient_data <- list(
    id = id,
    name = name,
    picture = patient_avatar,
    age = age,
    height = paste0(height, " cm"),
    weight = paste0(weight, " kg"),
    medical_history = list(
      pathologies = pathologies,
      examination_dates = examination_dates,
      doctors = doctors,
      doctors_avatars = doctors_avatars,
      disease_description = disease_description,
      disease_image = disease_image
    ),
    disease_id = disease_id,
    initial_conditions = state
  )
  saveRDS(object = patient_data, file = paste0(raw_folder, "patients_datas/patient_", id, ".rds"))
}

patient_generator(
  id = 1,
  name = "Patient: John Doe",
  age = "50 yrs",
  height = 183,
  weight = 72,
  gender = "male",
  disease_id = "hyperD3",
  pathologies = list(
    "Hyporeactivity, muscle aches, appetite loss, constipation, irritability",
    "Preliminary blood and urine analyses",
    "Mild left hydronephrosis"
  ),
  examination_dates = list(rep("", 3)),
  doctors = list(
    "Initial consultation",
    "Laboratory Findings",
    "Renal sonography"
  ),
  doctors_gender = list("male", "female", "male"),
  disease_description = list(
    "Mr. Doe presented with tiredness and hyporeactivity.
    Over the past few weeks, he had experienced fatigue, excessive thirst,
    muscle aches, loss of appetite, constipation and irritability. <br>
    Mr. Doe did not have any relevant past clinical history and was
    not taking any medication apart from over the counter supplements.
    Basic physical parameters were normal: BMI (21.5 kg/m2), blood
    pressure (120/70 mmHg) and heart rate (70 bpm).
    ",
    NULL,
    "Renal sonography revealed normal sized kidneys (right 10.cm, left 11cm),
    no nephrocalcinosis, but a mild left hydronephrosis."
    ),
  disease_image = list(
    NULL,
    "case_studies_img/patient1-1.svg",
    NULL
  )
)