diff --git a/R/CreateRunOptions.R b/R/CreateRunOptions.R
index 35d930ee681fd9fbe966c2f30d65082fe13e6636..7b943183b67a1518c2130452b9d6bb1f890000cb 100644
--- a/R/CreateRunOptions.R
+++ b/R/CreateRunOptions.R
@@ -1,69 +1,3 @@
-#*************************************************************************************************
-#' Creation of the RunOptions object required to the RunModel functions.
-#'
-#' Users wanting to use FUN_MOD functions that are not included in
-#' the package must create their own RunOptions object accordingly.
-#'
-#' ##### Initialisation options #####
-#'
-#' The model initialisation options can either be set to a default configuration or be defined by the user.
-#'
-#' This is done via three vectors: \cr \emph{IndPeriod_WarmUp}, \emph{IniStates}, \emph{IniResLevels}. \cr
-#' A default configuration is used for initialisation if these vectors are not defined.
-#'
-#' (1) Default initialisation options:
-#'
-#' \itemize{
-#' \item \emph{IndPeriod_WarmUp} default setting ensures a one-year warm-up using the time-steps preceding the \emph{IndPeriod_Run}.
-#' The actual length of this warm-up might be shorter depending on data availability (no missing value being allowed on model input series).
-#'
-#' \item \emph{IniStates} and \emph{IniResLevels} are automatically set to initialise all the model states at 0, except for the production and routing stores which are initialised at 50\% of their capacity. This initialisation is made at the very beginning of the model call (i.e. at the beginning of \emph{IndPeriod_WarmUp} or at the beginning of IndPeriod_Run if the warm-up period is disabled).
-#' }
-#'
-#' (2) Customisation of initialisation options:
-#'
-#' \itemize{
-#' \item \emph{IndPeriod_WarmUp} can be used to specify the indices of the warm-up period (within the time-series prepared in InputsModel). \cr
-#' - remark 1: for most common cases, indices corresponding to one or several years preceding \emph{IndPeriod_Run} are used (e.g. \emph{IndPeriod_WarmUp <- 1000:1365} and \emph{IndPeriod_Run <- 1366:5000)}. \cr
-#' However, it is also possible to perform a long-term initialisation if other indices than the warm-up ones are set in \emph{IndPeriod_WarmUp} (e.g. \emph{IndPeriod_WarmUp <- c( 1:5000 , 1:5000 , 1:5000 ,1000:1365 )}). \cr
-#' - remark 2: it is also possible to completely disable the warm-up period when using \emph{IndPeriod_WarmUp <- 0}.
-#'
-#' \item \emph{IniStates} and \emph{IniResLevels} can be used to specify the initial model states. \cr
-#' - remark 1: if \emph{IniStates} is used, all model states must be provided (e.g. 60 floats [mm] are required for GR4J, GR5J and GR6J; 60+2*NLayers floats [mm] are required for CemaNeigeGR4J, CemaNeigeGR5J and CemaNeigeGR6J; see fortran source code for details). \cr
-#' - remark 2: in addition to \emph{IniStates}, \emph{IniResLevels} allows to set the filling rate of the production and routing stores for the GR models. For instance for GR4J, GR5J and GR6J: \emph{IniResLevels <- c(0.3,0.5)} should be used to obtain initial fillings of 30\% and 50\% for the production and routing stores, respectively. \emph{IniResLevels} is optional and can only be used if \emph{IniStates} is also defined (the state values corresponding to these two stores in \emph{IniStates} are not used in such case). \cr \cr
-#' }
-#*************************************************************************************************
-#' @title Creation of the RunOptions object required to the RunModel functions
-#' @author Laurent Coron (June 2014)
-#' @seealso \code{\link{RunModel}}, \code{\link{CreateInputsModel}}, \code{\link{CreateInputsCrit}}, \code{\link{CreateCalibOptions}}
-#' @example tests/example_RunModel.R
-#' @encoding UTF-8
-#' @export
-#_FunctionInputs__________________________________________________________________________________
-#' @param FUN_MOD [function] hydrological model function (e.g. RunModel_GR4J, RunModel_CemaNeigeGR4J)
-#' @param InputsModel [object of class \emph{InputsModel}] see \code{\link{CreateInputsModel}} for details
-#' @param IndPeriod_WarmUp (optional) [numeric] index of period to be used for the model warm-up [-]
-#' @param IndPeriod_Run [numeric] index of period to be used for the model run [-]
-#' @param IniStates (optional) [numeric] vector of initial model states [mm]
-#' @param IniResLevels (optional) [numeric] vector of initial filling rates for production and routing stores (2 values between 0 and 1) [-]
-#' @param Outputs_Cal (optional) [character] vector giving the outputs needed for the calibration \cr (e.g. c("Qsim")), the least outputs the fastest the calibration
-#' @param Outputs_Sim (optional) [character] vector giving the requested outputs \cr (e.g. c("DatesR","Qsim","SnowPack")), default="all"
-#' @param RunSnowModule (optional) [boolean] option indicating whether CemaNeige should be activated, default=TRUE
-#' @param MeanAnSolidPrecip (optional) [numeric] vector giving the annual mean of average solid precipitation for each layer (computed from InputsModel if not defined) [mm/y]
-#' @param quiet (optional) [boolean] boolean indicating if the function is run in quiet mode or not, default=FALSE
-#_FunctionOutputs_________________________________________________________________________________
-#' @return [list] object of class \emph{RunOptions} containing the data required to evaluate the model outputs; it can include the following:
-#' \tabular{ll}{
-#' \emph{IndPeriod_WarmUp } \tab [numeric] index of period to be used for the model warm-up [-] \cr
-#' \emph{IndPeriod_Run } \tab [numeric] index of period to be used for the model run [-] \cr
-#' \emph{IniStates } \tab [numeric] vector of initial model states [mm] \cr
-#' \emph{IniResLevels } \tab [numeric] vector of initial filling rates for production and routing stores [-] \cr
-#' \emph{Outputs_Cal } \tab [character] character vector giving only the outputs needed for the calibration \cr
-#' \emph{Outputs_Sim } \tab [character] character vector giving the requested outputs \cr
-#' \emph{RunSnowModule } \tab [boolean] option indicating whether CemaNeige should be activated \cr
-#' \emph{MeanAnSolidPrecip} \tab [numeric] vector giving the annual mean of average solid precipitation for each layer [mm/y] \cr
-#' }
-#**************************************************************************************************'
CreateRunOptions <- function(FUN_MOD,InputsModel,IndPeriod_WarmUp=NULL,IndPeriod_Run,IniStates=NULL,IniResLevels=NULL,
Outputs_Cal=NULL,Outputs_Sim="all",RunSnowModule=TRUE,MeanAnSolidPrecip=NULL,quiet=FALSE){
@@ -166,8 +100,8 @@ CreateRunOptions <- function(FUN_MOD,InputsModel,IndPeriod_WarmUp=NULL,IndPeriod
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 <- 3*24*20; }
- if("daily" %in% ObjectClass){ NState <- 3*20 + 2*NLayers; }
+ if("hourly" %in% ObjectClass){ NState <- 3*24*20 + 7; }
+ if("daily" %in% ObjectClass){ if (identical(FUN_MOD,RunModel_GR5J)){NState <- 2*20 + 2*NLayers + 7; } else {NState <- 3*20 + 2*NLayers + 7; }}
if("monthly" %in% ObjectClass){ NState <- 2; }
if("yearly" %in% ObjectClass){ NState <- 1; }
}
@@ -204,7 +138,7 @@ CreateRunOptions <- function(FUN_MOD,InputsModel,IndPeriod_WarmUp=NULL,IndPeriod
if(identical(FUN_MOD,RunModel_GR6J) | identical(FUN_MOD,RunModel_CemaNeigeGR6J)){
Outputs_all <- c(Outputs_all,"PotEvap","Precip","Prod","AE","Perc","PR","Q9","Q1","Rout","Exch","AExch","QR","QR1","Exp","QD","Qsim"); }
if(identical(FUN_MOD,RunModel_GR2M)){
- Outputs_all <- c(Outputs_all,"PotEvap","Precip","Qsim"); }
+ Outputs_all <- c(Outputs_all,"PotEvap","Precip","AE","Perc","P3","Exch","Prod","Rout","Qsim"); }
if(identical(FUN_MOD,RunModel_GR1A)){
Outputs_all <- c(Outputs_all,"PotEvap","Precip","Qsim"); }
if("CemaNeige" %in% ObjectClass){