CreateRunOptions <- function(FUN_MOD, InputsModel, IndPeriod_WarmUp = NULL, IndPeriod_Run,
                             IniStates = NULL, IniResLevels = NULL, 
                             Outputs_Cal = NULL, Outputs_Sim = "all",
                             RunSnowModule, MeanAnSolidPrecip = NULL,
                             warnings = TRUE, verbose = TRUE) {
  
  if (!missing(RunSnowModule)) {
    warning("argument RunSnowModule is deprecated; please adapt FUN_MOD instead.", call. = FALSE)
  }
  
  ObjectClass <- NULL
  
  ##check_FUN_MOD
  BOOL <- FALSE;
  if (identical(FUN_MOD, RunModel_GR4H)) {
    ObjectClass <- c(ObjectClass, "GR", "hourly")
    BOOL <- TRUE
  }
  if (identical(FUN_MOD, RunModel_GR4J) | identical(FUN_MOD, RunModel_GR5J) | identical(FUN_MOD, RunModel_GR6J)) {
    ObjectClass <- c(ObjectClass, "GR", "daily")
    BOOL <- TRUE
  }
  if (identical(FUN_MOD, RunModel_GR2M)) {
    ObjectClass <- c(ObjectClass, "GR", "monthly")
    BOOL <- TRUE
  }
  if (identical(FUN_MOD, RunModel_GR1A)) {
    ObjectClass <- c(ObjectClass, "GR", "yearly")
    BOOL <- TRUE
  }
  if (identical(FUN_MOD, RunModel_CemaNeige)) {
    ObjectClass <- c(ObjectClass, "CemaNeige", "daily")
    BOOL <- TRUE
  }
  if (identical(FUN_MOD, RunModel_CemaNeigeGR4J) | identical(FUN_MOD, RunModel_CemaNeigeGR5J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J)) {
    ObjectClass <- c(ObjectClass, "GR", "CemaNeige", "daily")
    BOOL <- TRUE
  }
  if (!BOOL) {
    stop("incorrect FUN_MOD for use in CreateRunOptions \n")
    return(NULL)
  }
  
  ##check_InputsModel
  if (!inherits(InputsModel, "InputsModel")) {
    stop("InputsModel must be of class 'InputsModel' \n")
    return(NULL)
  }
  if ("GR" %in% ObjectClass & !inherits(InputsModel, "GR")) {
    stop("InputsModel must be of class 'GR' \n")
    return(NULL)
  }
  if ("CemaNeige" %in% ObjectClass &
      !inherits(InputsModel, "CemaNeige")) {
    stop("InputsModel must be of class 'CemaNeige' \n")
    return(NULL)
  }
  if ("hourly" %in% ObjectClass &
      !inherits(InputsModel, "hourly")) {
    stop("InputsModel must be of class 'hourly' \n")
    return(NULL)
  }
  if ("daily" %in% ObjectClass & !inherits(InputsModel, "daily")) {
    stop("InputsModel must be of class 'daily' \n")
    return(NULL)
  }
  if ("monthly" %in% ObjectClass &
      !inherits(InputsModel, "monthly")) {
    stop("InputsModel must be of class 'monthly' \n")
    return(NULL)
  }
  if ("yearly" %in% ObjectClass &
      !inherits(InputsModel, "yearly")) {
    stop("InputsModel must be of class 'yearly' \n")
    return(NULL)
  }
  
  
  ##check_IndPeriod_Run
  if (!is.vector(IndPeriod_Run)) {
    stop("IndPeriod_Run must be a vector of numeric values \n")
    return(NULL)
  }
  if (!is.numeric(IndPeriod_Run)) {
    stop("IndPeriod_Run must be a vector of numeric values \n")
    return(NULL)
  }
  if (identical(as.integer(IndPeriod_Run), as.integer(seq(from = IndPeriod_Run[1], to = tail(IndPeriod_Run, 1), by = 1))) == FALSE) {
    stop("IndPeriod_Run must be a continuous sequence of integers \n")
    return(NULL)
  }
  if (storage.mode(IndPeriod_Run) != "integer") {
    stop("IndPeriod_Run should be of type integer \n")
    return(NULL)
  }
  
  
  ##check_IndPeriod_WarmUp
  WTxt <- NULL
  if (is.null(IndPeriod_WarmUp)) {
    WTxt <- paste0(WTxt,"\t Model warm up period not defined -> default configuration used \n")
    ##If_the_run_period_starts_at_the_very_beginning_of_the_time_series
    if (IndPeriod_Run[1] == as.integer(1)) {
      IndPeriod_WarmUp <- as.integer(0)
      WTxt <- paste0(WTxt,"\t    No data were found for model warm up! \n")
      ##We_look_for_the_longest_period_preceeding_the_run_period_with_a_maximum_of_one_year
    } else {
      TmpDateR0 <- InputsModel$DatesR[IndPeriod_Run[1]]
      TmpDateR  <- TmpDateR0 - 365 * 24 * 60 * 60
      ### minimal date to start the warmup
      if (format(TmpDateR, format = "%d") != format(TmpDateR0, format = "%d")) {
        ### leap year
        TmpDateR <- TmpDateR - 1 * 24 * 60 * 60
      }
      IndPeriod_WarmUp <- which(InputsModel$DatesR == max(InputsModel$DatesR[1], TmpDateR)):(IndPeriod_Run[1] - 1)
      if ("hourly"  %in% ObjectClass) {
        TimeStep <- as.integer(60 * 60)
      }
      if ("daily"   %in% ObjectClass) {
        TimeStep <- as.integer(24 * 60 * 60)
      }
      if ("monthly" %in% ObjectClass) {
        TimeStep <- as.integer(30.44 * 24 * 60 * 60)
      }
      if ("yearly"  %in% ObjectClass) {
        TimeStep <- as.integer(365.25 * 24 * 60 * 60)
      }
      if (length(IndPeriod_WarmUp) * TimeStep / (365 * 24 * 60 * 60) >= 1) {
        WTxt <- paste0(WTxt, "\t    The year preceding the run period is used \n")
      } else {
        WTxt <- paste0(WTxt, "\t    Less than a year (without missing values) was found for model warm up: \n")
        WTxt <- paste0(WTxt, "\t    (", length(IndPeriod_WarmUp), " time-steps are used for initialisation) \n")
      }
    }
  }
  if (!is.null(IndPeriod_WarmUp)) {
    if (!is.vector(IndPeriod_WarmUp)) {
      stop("'IndPeriod_WarmUp' must be a vector of numeric values \n")
      return(NULL)
    }
    if (!is.numeric(IndPeriod_WarmUp)) {
      stop("'IndPeriod_WarmUp' must be a vector of numeric values \n")
      return(NULL)
    }
    if (storage.mode(IndPeriod_WarmUp) != "integer") {
      stop("'IndPeriod_WarmUp' should be of type integer \n")
      return(NULL)
    }
    if (identical(IndPeriod_WarmUp, as.integer(0)) & verbose) {
      message(paste0(WTxt, "\t No warm up period is used \n"))
    }
    if ((IndPeriod_Run[1] - 1) != tail(IndPeriod_WarmUp, 1) & !identical(IndPeriod_WarmUp, as.integer(0))) {
      WTxt <- paste0(WTxt, "\t Model warm up period is not directly before the model run period \n")
    }
  }
  if (!is.null(WTxt) & warnings) {
    warning(WTxt)
  }
  
  
  ## check IniResLevels    
  if ("GR" %in% ObjectClass & ("monthly" %in% ObjectClass | "daily" %in% ObjectClass | "hourly" %in% ObjectClass)) {
    if (!is.null(IniResLevels)) {
      if (!is.vector(IniResLevels) | !is.numeric(IniResLevels) | any(is.na(IniResLevels))) {
        stop("IniResLevels must be a vector of numeric values \n")
        return(NULL)
      }
      if ((identical(FUN_MOD, RunModel_GR4H) |
           identical(FUN_MOD, RunModel_GR4J) | identical(FUN_MOD, RunModel_CemaNeigeGR4J) |
           identical(FUN_MOD, RunModel_GR5J) | identical(FUN_MOD, RunModel_CemaNeigeGR5J) |
           identical(FUN_MOD, RunModel_GR2M)) &
          length(IniResLevels) != 2) {
        stop("The length of IniResLevels must be 2 for the chosen FUN_MOD \n")
        return(NULL)
      }
      if ((identical(FUN_MOD,RunModel_GR6J) | identical(FUN_MOD,RunModel_CemaNeigeGR6J)) &
          length(IniResLevels) != 3) {
        stop("The length of IniResLevels must be 3 for the chosen FUN_MOD \n")
        return(NULL)
      }
    } else if (is.null(IniStates)) {
      if (identical(FUN_MOD, RunModel_GR6J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J)) {
        IniResLevels <- as.double(c(0.3, 0.5, 0))
      } else {
        IniResLevels <- as.double(c(0.3, 0.5, NA))
      }
    }
  } else {
    if (!is.null(IniResLevels)) {
      stop("IniResLevels can only be used with monthly or daily or hourly GR models \n")
    }
  }
  ## check IniStates
  if (is.null(IniStates) & is.null(IniResLevels) & warnings) {
    warning("\t Model states initialisation not defined -> default configuration used \n")
  }
  if (!is.null(IniStates) & !is.null(IniResLevels) & warnings) {
    warning("\t IniStates and IniResLevels are both defined -> Store levels are taken from IniResLevels \n")
  }
  if ("CemaNeige" %in% ObjectClass) {
    NLayers <- length(InputsModel$LayerPrecip)
  } else {
    NLayers <- 0
  }
  NState <- NULL
  if ("GR" %in% ObjectClass | "CemaNeige" %in% ObjectClass) {
    if ("hourly"  %in% ObjectClass) {
      NState <- 7 + 3 * 24 * 20
    }
    if ("daily"   %in% ObjectClass) {
      NState <- 7 + 3 * 20 + 2 * NLayers
    }
    if ("monthly" %in% ObjectClass) {
      NState <- 2
    }
    if ("yearly"  %in% ObjectClass) {
      NState <- 1
    }
  }
  if (!is.null(IniStates)) {
    
    if (!inherits(IniStates, "IniStates")) {
      stop("IniStates must be an object of class IniStates\n")
      return(NULL)
    }
    if (sum(ObjectClass %in% class(IniStates)) < 2) {
      stop(paste0("Non convenient IniStates for this FUN_MOD\n"))
      return(NULL)
    }
    if (identical(FUN_MOD, RunModel_GR1A) & !is.null(IniStates)) { ## GR1A
      stop(paste0("IniStates is not available for this FUN_MOD\n"))
      return(NULL)
    }
    if ((identical(FUN_MOD, RunModel_GR5J) | identical(FUN_MOD, RunModel_CemaNeigeGR5J)) & !all(is.na(IniStates$UH$UH1))) { ## GR5J
      stop(paste0("Non convenient IniStates for this FUN_MOD. In IniStates, UH1 has to be a vector of NA for GR5J \n"))
      return(NULL)
    }
    if ((identical(FUN_MOD, RunModel_GR6J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J)) & is.na(IniStates$Store$Exp)) { ## GR6J
      stop(paste0("Non convenient IniStates for this FUN_MOD. GR6J needs an exponential store value in IniStates \n"))
      return(NULL)
    }
    if (!(identical(FUN_MOD, RunModel_GR6J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J)) & !is.na(IniStates$Store$Exp)) { ## except GR6J
      stop(paste0("Non convenient IniStates for this FUN_MOD. No exponential store value needed in IniStates \n"))
      return(NULL)
    }
    # if (length(na.omit(unlist(IniStates))) != NState) {
    #   stop(paste0("The length of IniStates must be ", NState, " for the chosen FUN_MOD \n"))
    #   return(NULL)
    # }
    if (!"CemaNeige" %in% ObjectClass & any(is.na(IniStates$CemaNeigeLayers$G  ))) {
      IniStates$CemaNeigeLayers$G   <- NULL
    }
    if (!"CemaNeige" %in% ObjectClass & any(is.na(IniStates$CemaNeigeLayers$eTG))) {
      IniStates$CemaNeigeLayers$eTG <- NULL
    }
    IniStates$Store$Rest <- rep(NA, 4)
    IniStates <- unlist(IniStates)
    IniStates[is.na(IniStates)] <- 0
    if ("monthly" %in% ObjectClass) {
      IniStates <- IniStates[seq_len(NState)]
    }
  } else {
    IniStates <- as.double(rep(0.0, NState))
  }
  
  
  ##check_Outputs_Cal_and_Sim
  
  ##Outputs_all
  Outputs_all <- NULL
  if (identical(FUN_MOD,RunModel_GR4H)) {
    Outputs_all <- c(Outputs_all,"PotEvap","Precip","Prod","AE","Perc","PR","Q9","Q1","Rout","Exch","AExch","QR","QD","Qsim")
  }
  if (identical(FUN_MOD,RunModel_GR4J) | identical(FUN_MOD,RunModel_CemaNeigeGR4J)) {
    Outputs_all <- c(Outputs_all,"PotEvap", "Precip", "Prod", "Pn", "Ps", "AE", "Perc", "PR", "Q9", "Q1", "Rout", "Exch",
                     "AExch1", "AExch2", "AExch", "QR", "QD", "Qsim")
  }
  if (identical(FUN_MOD,RunModel_GR5J) | identical(FUN_MOD,RunModel_CemaNeigeGR5J)) {
    Outputs_all <- c(Outputs_all,"PotEvap", "Precip", "Prod", "Pn", "Ps", "AE", "Perc", "PR", "Q9", "Q1", "Rout", "Exch",
                     "AExch1", "AExch2", "AExch", "QR", "QD", "Qsim")
  }
  if (identical(FUN_MOD,RunModel_GR6J) | identical(FUN_MOD,RunModel_CemaNeigeGR6J)) {
    Outputs_all <- c(Outputs_all,"PotEvap", "Precip", "Prod", "Pn", "Ps", "AE", "Perc", "PR", "Q9", "Q1", "Rout", "Exch",
                     "AExch1", "AExch2", "AExch", "QR", "QRExp", "Exp", "QD", "Qsim")
  }
  if (identical(FUN_MOD,RunModel_GR2M)) {
    Outputs_all <- c(Outputs_all,"PotEvap", "Precip", "AE", "Pn", "Perc", "PR", "Exch", "Prod", "Rout", "Qsim")
  }
  if (identical(FUN_MOD,RunModel_GR1A)) {
    Outputs_all <- c(Outputs_all,"PotEvap","Precip","Qsim")
  }
  if ("CemaNeige" %in% ObjectClass) {
    Outputs_all <- c(Outputs_all,"Pliq","Psol","SnowPack","ThermalState","Gratio","PotMelt","Melt","PliqAndMelt", "Temp")
  }
  
  ##check_Outputs_Sim
  if (!is.vector(Outputs_Sim)) {
    stop("Outputs_Sim must be a vector of characters \n")
    return(NULL)
  }
  if (!is.character(Outputs_Sim)) {
    stop("Outputs_Sim must be a vector of characters \n")
    return(NULL)
  }
  if (sum(is.na(Outputs_Sim)) != 0) {
    stop("Outputs_Sim must not contain NA \n")
    return(NULL)
  }
  if ("all" %in% Outputs_Sim) {
    Outputs_Sim <- c("DatesR", Outputs_all, "StateEnd")
  }
  Test <- which(Outputs_Sim %in% c("DatesR", Outputs_all, "StateEnd") == FALSE)
  if (length(Test) != 0) {
    stop(paste0( "Outputs_Sim is incorrectly defined: ",
                 paste(Outputs_Sim[Test], collapse = ", "), " not found \n"))
    return(NULL)
    
  }
  Outputs_Sim <- Outputs_Sim[!duplicated(Outputs_Sim)]
  
  
  ##check_Outputs_Cal
  if (is.null(Outputs_Cal)) {
    if ("GR" %in% ObjectClass) {
      Outputs_Cal <- c("Qsim")
    }
    if ("CemaNeige" %in% ObjectClass) {
      Outputs_Cal <- c("all")
    }
    if ("GR" %in% ObjectClass &
        "CemaNeige" %in% ObjectClass) {
      Outputs_Cal <- c("PliqAndMelt", "Qsim")
    }
  } else {
    if (!is.vector(Outputs_Cal)) {
      stop("Outputs_Cal must be a vector of characters \n")
      return(NULL)
    }
    if (!is.character(Outputs_Cal)) {
      stop("Outputs_Cal must be a vector of characters \n")
      return(NULL)
    }
    if (sum(is.na(Outputs_Cal)) != 0) {
      stop("Outputs_Cal must not contain NA \n")
      return(NULL)
    }
  }
  if ("all" %in% Outputs_Cal) {
    Outputs_Cal <- c("DatesR", Outputs_all, "StateEnd")
    
  }
  Test <-
    which(Outputs_Cal %in% c("DatesR", Outputs_all, "StateEnd") == FALSE)
  if (length(Test) != 0) {
    stop(paste0("Outputs_Cal is incorrectly defined: ",
                paste(Outputs_Cal[Test], collapse = ", "), " not found \n"))
    return(NULL)
    
  }
  Outputs_Cal <- Outputs_Cal[!duplicated(Outputs_Cal)]
  
  
  
  ##check_MeanAnSolidPrecip
  if ("CemaNeige" %in% ObjectClass & is.null(MeanAnSolidPrecip)) {
    NLayers <- length(InputsModel$LayerPrecip)
    SolidPrecip <- NULL
    for (iLayer in 1:NLayers) {
      if (iLayer == 1) {
        SolidPrecip <-
          InputsModel$LayerFracSolidPrecip[[1]] * InputsModel$LayerPrecip[[iLayer]] /
          NLayers
      } else {
        SolidPrecip <- SolidPrecip + InputsModel$LayerFracSolidPrecip[[iLayer]] * InputsModel$LayerPrecip[[iLayer]] / NLayers
      }
    }
    Factor <- NULL
    if (inherits(InputsModel, "hourly")) {
      Factor <- 365.25 * 24
    }
    if (inherits(InputsModel, "daily")) {
      Factor <- 365.25
    }
    if (inherits(InputsModel, "monthly")) {
      Factor <- 12
    }
    if (inherits(InputsModel, "yearly")) {
      Factor <- 1
    }
    if (is.null(Factor)) {
      stop("InputsModel must be of class 'hourly', 'daily', 'monthly' or 'yearly' \n")
      return(NULL)
    }
    MeanAnSolidPrecip <- rep(mean(SolidPrecip) * Factor, NLayers)
    ### default value: same Gseuil for all layers
    if (warnings) {
      warning("\t MeanAnSolidPrecip not defined -> it was automatically set to c(",
              paste(round(MeanAnSolidPrecip), collapse = ","), ") \n")
    }
  }
  if ("CemaNeige" %in% ObjectClass & !is.null(MeanAnSolidPrecip)) {
    if (!is.vector(MeanAnSolidPrecip)) {
      stop(paste0("MeanAnSolidPrecip must be a vector of numeric values \n"))
      return(NULL)
    }
    if (!is.numeric(MeanAnSolidPrecip)) {
      stop(paste0("MeanAnSolidPrecip must be a vector of numeric values \n"))
      return(NULL)
    }
    if (length(MeanAnSolidPrecip) != NLayers) {
      stop(paste0("MeanAnSolidPrecip must be a numeric vector of length ", NLayers, " \n"))
      return(NULL)
    }
  }
  
  
  ##check_PliqAndMelt
  if ("GR" %in% ObjectClass & "CemaNeige" %in% ObjectClass) {
    if ("PliqAndMelt" %in% Outputs_Cal == FALSE & "all" %in% Outputs_Cal == FALSE) {
      WTxt <- NULL
      WTxt <- paste0(WTxt, "\t PliqAndMelt was not defined in Outputs_Cal but is needed to feed the hydrological model with the snow modele outputs \n")
      WTxt <- paste0(WTxt, "\t -> it was automatically added \n")
      if (!is.null(WTxt) & warnings) {
        warning(WTxt)
      }
      Outputs_Cal <- c(Outputs_Cal, "PliqAndMelt")
    }
    if ("PliqAndMelt" %in% Outputs_Sim == FALSE & "all" %in% Outputs_Sim == FALSE) {
      WTxt <- NULL
      WTxt <- paste0(WTxt, "\t PliqAndMelt was not defined in Outputs_Sim but is needed to feed the hydrological model with the snow modele outputs \n")
      WTxt <- paste0(WTxt, "\t -> it was automatically added \n")
      if (!is.null(WTxt) & warnings) {
        warning(WTxt)
      }
      Outputs_Sim <- c(Outputs_Sim, "PliqAndMelt")
    }
  }
  
  
  ##Create_RunOptions
  RunOptions <- list(IndPeriod_WarmUp = IndPeriod_WarmUp,
                     IndPeriod_Run = IndPeriod_Run,
                     IniStates = IniStates,
                     IniResLevels = IniResLevels,
                     Outputs_Cal = Outputs_Cal,
                     Outputs_Sim = Outputs_Sim)
  
  if ("CemaNeige" %in% ObjectClass) {
    RunOptions <-
      c(RunOptions, list(MeanAnSolidPrecip = MeanAnSolidPrecip))
  }
  class(RunOptions) <- c("RunOptions", ObjectClass)
  
  return(RunOptions)
  
  
}