R/SimulateBreathID.R

In dmenne/d13cbreath: Reads and Evaluates Gastric Emptying 13C Breath Test Data

#' @title Simulated BreathID record for testing
#' @description A time series that can be fit by exponential beta
#' @name SimulateBreathId
#' @return A record that is a modified version of the provided sample
#' record, with additional fields \code{Name, FirstName, Initials, FileName}
#' @seealso \code{\link{ReadBreathId}}, \code{\link{AddSimulatedBreathTestRecord}}
#' @export
SimulateBreathId = function() {
  # To be sure we get the format right, we read one sample from BreathID
  filename = system.file("extdata", "350_20043_0_GER.txt",
                         package = "D13CBreath")
  bid = ReadBreathId(filename)
  bid$FirstName = RandomName()
  bid$Name = RandomName()
  bid$Initials = paste0(str_sub(bid$FirstName,1,1),
                       str_sub(bid$Name,1,1))
  bid$FileName = RandomFile()
  bid$StartTime = Sys.time() -  60 * 60 * 24 * 200 * runif(1)
  bid$RecordDate = as.Date(bid$StartTime)
  bid$EndTime = bid$StartTime + rnorm(1,60 * 100,20)
  bid$PatientID = sample(c("Alpha","Beta","Gamma","Delta"),1)
  bid$TestNo = sample(20000:30000,1)
  bid$Height = round(rnorm(1,180,5))
  bid$Weight = round(rnorm(1,70,5))
  bid$Device = "BreathID"
  start = list(m = 20,k = 1 / 100,beta = 2)
  m = rnorm(1,start$m,start$m * 0.1)
  k = rnorm(1,start$k,start$k * 0.1)
  beta = rnorm(1,start$beta,start$beta * 0.05)
  
  bid$Data$DOB = as.numeric(ExpBeta(bid$Data$Time,100,m,k,beta)) +
    rnorm(length(bid$Data$Time),0,0.5)
  bid$Data$PDR = bid$Data$DOB * rnorm(1,1.2,0.1)
  bid$Data$PDRfit = NULL
  bid$Data$CPDR = NULL
  bid$Data$CPDRfit = NULL
  bid
}


#' @title Adds simulated breath test record to the database
#' @name AddSimulatedBreathTestRecord
#' @description Creates a simulated data record, computes several fit
#' parameters, and appends these to the database
#' @param con connection to sqlite database
#' @seealso \code{\link{ReadBreathId}}, \code{\link{SimulateBreathId}},
#' \code{\link{CreateSimulatedBreathTestDatabase}}
#'
#' @examples
#' # This example does the same as the function \code{CreateSimulatedBreathTestDatabase}
#' if (exists("con"))
#'   suppressWarnings(dbDisconnect(con))
#' sqlitePath = tempfile(pattern = "Gastrobase", tmpdir = tempdir(), fileext = ".sqlite")
#' unlink(sqlitePath)
#' CreateEmptyBreathTestDatabase(sqlitePath)
#' con = OpenSqliteConnection(sqlitePath)
#' add = try (
#'   for (i in 1:10)
#'     AddSimulatedBreathTestRecord(con),silent = TRUE)
#' dbDisconnect(con)
#' @export
AddSimulatedBreathTestRecord = function(con) {
  bid = SimulateBreathId()
  BreathTestRecordToDatabase(bid,con)
}


#' @title Creates a database with simulated breath tests
#' @name CreateSimulatedBreathTestDatabase
#' @description Creates a database with simulated breath test records.
#' If sqlitePath is NULL, it is created in temporary directory.
#' To create a file in the default path, use
#' \code{CreateSimulatedBreathTestDatabase(getOption("Gastrobase2SqlitePath"))}
#' @param sqlitePath Path to created sqlite file.
#' @return File name of simulated database
#' @export
CreateSimulatedBreathTestDatabase = function(sqlitePath = NULL) {
  set.seed(4711)
  if (is.null(sqlitePath))
    sqlitePath = tempfile(pattern = "Gastrobase", tmpdir = tempdir(), fileext = ".sqlite")
  # ***************** Debug ***********************************
  #print("DDDDDDDDDDDDD")
  #sqlitePath = "C:/tmp/GastrobaseTest.sqlite"
  unlink(sqlitePath)
  CreateEmptyBreathTestDatabase(sqlitePath)
  con = OpenSqliteConnection(sqlitePath)
  add = try(
    for (i in 1:10)
      AddSimulatedBreathTestRecord(con),silent = TRUE
  )
  if (inherits(add,"try-error")) {
    stop(paste(
      "CreateSimulatedBreathTestDatabase", attr(add,"condition")$message
    ))
  }
  setting = data.frame(
    SettingID = c("BlueItem","GreenItem","OrangeItem","RedItem"),
    Value = c("Record_1","Record_2","Record_3","Patient_Gamma"),
    stringsAsFactors = FALSE
  )
  q = "INSERT INTO Setting VALUES($SettingID, $Value)"
  try(dbExecute(con, q, params = setting), silent = TRUE)

  # Ok
  RebuildPopulationFitDatabase(con)
  dbDisconnect(con)
  sqlitePath
}

RandomName = function(nLetters = 6) {
  paste0(sample(LETTERS[1:26],1,TRUE),
         paste0(sample(letters[1:26],nLetters - 1,TRUE),collapse = ""))
}
RandomFile = function(ext = "txt") {
  paste0(paste(
    sample(100:999,1,TRUE),sample(10000:99999,1,TRUE),
    sample(1:9,1),sep = "_"
  ),".",ext)
}