R/runTempTool.R

In skfogg/temptool: Run "TempTool" Stream Temperature Model

#' run TempTool
#'
#' @param odbcConnection RODBC object
#' @param binStats data frame returned from hyporheicBins()
#' @param channelVolume numeric
#' @param channelSurfaceArea numeric
#' @param surfaceShade numeric
#' @param firstBin numeric
#' @param lastBin numeric
#' @param timeStep numeric
#' @param yearsToRun numeric (years)
#' @param runID character
#' @param outputIndex lubridate object
#' @param internal print java output? logical
#'
#' @return list of tts objects from each model cell
#' @export

runTempTool <- function(odbcConnection,
                         binStats,
                         initTemps = NULL,
                         channelVolume,
                         channelSurfaceArea,
                         surfaceShade,
                         firstBin,
                         lastBin,
                         timeStep,
                         yearsToRun,
                         outputInterval,
                         runID = "",
                         outputIndex = NULL,
                         internal = TRUE){

  require(RODBC)
  require(lubridate)
  require(zoo)
  require(xts)
  require(hydrogeom)

  stoppingCondition <- (yearsToRun * 86400 * 365.25)/timeStep
  if(is.null(outputIndex)) outputIndex <- seq(mdy_hms("01-01-2014 00:00:00"), by = outputInterval, length.out = (86400/outputInterval)*yearsToRun*365.25)

  setSkeleton(firstBin, lastBin, odbcConnection)
  setParameters(firstBin, lastBin, odbcConnection, initTemps, surfaceShade, channelSurfaceArea, channelVolume, binStats)
  setTiming(odbcConnection, timeStep, yearsToRun, outputInterval)


  ### RUN MODEL ###
  #shell("cd D:\\Users\\sarah.fogg\\Desktop\\TempToolThatWorks && java -jar TempToolFour_March2015.jar", intern=TRUE)
  shell("cd C:\\Users\\t24x137\\Desktop\\Old Tower Desktop Folders\\TempToolThatWorks && java -jar TempToolFour_March2015.jar", intern=TRUE)

  connect <- odbcConnect("TempToolFourANSI", uid="root", pwd="poolelab")

  assign("cTemp", tts(odbcConnection = connect, holonName = "channel_0001", tableName = "temp_signal_output", runID = runID, xtsIndex = outputIndex))

  for(z in firstBin:lastBin){
    if(z < 10){
      assign(paste0("tsz", z, "Temp"), tts(odbcConnection = connect,
                                           holonName = paste0("hyporheic_000", z),
                                           tableName = "temp_signal_output",
                                           runID = runID,
                                           xtsIndex = outputIndex))
    } else {
      assign(paste0("tsz", z, "Temp"), tts(odbcConnection = connect,
                                           holonName = paste0("hyporheic_00", z),
                                           tableName = "temp_signal_output",
                                           runID = runID,
                                           xtsIndex = outputIndex))
    }
  }

  # # QUERY ALL TEMPERATURE OUTPUT
  # assign(paste0("channelTemp_run", runID), stateValSeries(connect, "TEMP", "channel_0001", "temp_signal_output", runID = runID, xtsIndex = outputIndex))
  #
  # for(z in firstBin:lastBin){
  #   if(z < 10){
  #     assign(paste0("hypo", z,"Temp_run", runID), stateValSeries(connect, "TEMP", paste0("hyporheic_000", z), "temp_signal_output", runID = runID, xtsIndex = outputIndex))
  #   } else {
  #     assign(paste0("hypo", z,"Temp_run", runID), stateValSeries(connect, "TEMP", paste0("hyporheic_00", z), "temp_signal_output", runID = runID, xtsIndex = outputIndex))
  #   }
  # }


  # CREATE LIST OF ALL RUN DATA
  objectNames <- c("cTemp", paste0("tsz", firstBin:lastBin, "Temp"))
  # assign(paste0("output_run", runID), lapply(objectNames, get))

  names(objectNames) <- objectNames
  outList <- as.list(objectNames)

  for(i in 1:length(objectNames)){
    outList[[i]] <- get(objectNames[i])
  }


  return(outList)

  }