diff --git a/NAMESPACE b/NAMESPACE
index 0a7cdfe3151eacd4acffa393cae5d82aa0d76c3f..7072ef735537f9b6ed843d2eaca9ead05693e05a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,7 +10,6 @@ useDynLib(airGR)
#####################################
export(Calibration)
export(Calibration_Michel)
-export(Calibration_optim)
export(CreateCalibOptions)
export(CreateInputsCrit)
export(CreateInputsModel)
diff --git a/R/Calibration_optim.R b/R/Calibration_optim.R
deleted file mode 100644
index 14fb6eceefb5e2f6940d19fcebc72936cd14ab99..0000000000000000000000000000000000000000
--- a/R/Calibration_optim.R
+++ /dev/null
@@ -1,152 +0,0 @@
-#*************************************************************************************************
-#' Calibration algorithm which minimises the error criterion. \cr
-#' \cr
-#' The algorithm is based on the "optim" function from the "stats" R-package
-#' (using method="L-BFGS-B", i.e. a local optimization quasi-Newton method).
-#'
-#' To optimise the exploration of the parameter space, transformation functions are used to convert
-#' the model parameters. This is done using the TransfoParam functions.
-#*************************************************************************************************
-#' @title Calibration algorithm which minimises the error criterion using the stats::optim function
-#' @author Laurent Coron (August 2013)
-#' @example tests/example_Calibration_optim.R
-#' @seealso \code{\link{Calibration}}, \code{\link{Calibration_Michel}},
-#' \code{\link{RunModel_GR4J}}, \code{\link{TransfoParam_GR4J}}, \code{\link{ErrorCrit_RMSE}},
-#' \code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}},
-#' \code{\link{CreateInputsCrit}}, \code{\link{CreateCalibOptions}}.
-#' @encoding UTF-8
-#' @export
-#_FunctionInputs__________________________________________________________________________________
-#' @param InputsModel [object of class \emph{InputsModel}] see \code{\link{CreateInputsModel}} for details
-#' @param RunOptions [object of class \emph{RunOptions}] see \code{\link{CreateRunOptions}} for details
-#' @param InputsCrit [object of class \emph{InputsCrit}] see \code{\link{CreateInputsCrit}} for details
-#' @param CalibOptions [object of class \emph{CalibOptions}] see \code{\link{CreateCalibOptions}} for details
-#' @param FUN_MOD [function] hydrological model function (e.g. RunModel_GR4J, RunModel_CemaNeigeGR4J)
-#' @param FUN_CRIT [function] error criterion function (e.g. ErrorCrit_RMSE, ErrorCrit_NSE)
-#' @param FUN_TRANSFO (optional) [function] model parameters transformation function, if the FUN_MOD used is native in the package FUN_TRANSFO is automatically defined
-#' @param quiet (optional) [boolean] boolean indicating if the function is run in quiet mode or not, default=FALSE
-#_FunctionOutputs_________________________________________________________________________________
-#' @return [list] list containing the function outputs organised as follows:
-#' \tabular{ll}{
-#' \emph{$ParamFinalR } \tab [numeric] parameter set obtained at the end of the calibration \cr
-#' \emph{$CritFinal } \tab [numeric] error criterion obtained at the end of the calibration \cr
-#' \emph{$Nruns } \tab [numeric] number of model runs done during the calibration \cr
-#' \emph{$CritName } \tab [character] name of the calibration criterion \cr
-#' \emph{$CritBestValue} \tab [numeric] theoretical best criterion value \cr
-#' }
-#**************************************************************************************************
-Calibration_optim <- function(InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_TRANSFO=NULL,quiet=FALSE){
-
-
- ##_check_class
- if(inherits(InputsModel,"InputsModel")==FALSE){ stop("InputsModel must be of class 'InputsModel' \n"); return(NULL); }
- if(inherits(RunOptions,"RunOptions")==FALSE){ stop("RunOptions must be of class 'RunOptions' \n"); return(NULL); }
- if(inherits(InputsCrit,"InputsCrit")==FALSE){ stop("InputsCrit must be of class 'InputsCrit' \n"); return(NULL); }
- if(inherits(CalibOptions,"CalibOptions")==FALSE){ stop("CalibOptions must be of class 'CalibOptions' \n"); return(NULL); }
- if(inherits(CalibOptions,"optim")==FALSE){ stop("CalibOptions must be of class 'optim' if Calibration_optim is used \n"); return(NULL); }
-
-
- ##_check_FUN_TRANSFO
- if(is.null(FUN_TRANSFO)){
- if(identical(FUN_MOD,RunModel_GR4H )){ FUN_TRANSFO <- TransfoParam_GR4H ; }
- if(identical(FUN_MOD,RunModel_GR4J )){ FUN_TRANSFO <- TransfoParam_GR4J ; }
- if(identical(FUN_MOD,RunModel_GR5J )){ FUN_TRANSFO <- TransfoParam_GR5J ; }
- if(identical(FUN_MOD,RunModel_GR6J )){ FUN_TRANSFO <- TransfoParam_GR6J ; }
- if(identical(FUN_MOD,RunModel_GR2M )){ FUN_TRANSFO <- TransfoParam_GR2M ; }
- if(identical(FUN_MOD,RunModel_GR1A )){ FUN_TRANSFO <- TransfoParam_GR1A ; }
- if(identical(FUN_MOD,RunModel_CemaNeige )){ FUN_TRANSFO <- TransfoParam_CemaNeige; }
- if(identical(FUN_MOD,RunModel_CemaNeigeGR4J) | identical(FUN_MOD,RunModel_CemaNeigeGR5J) | identical(FUN_MOD,RunModel_CemaNeigeGR6J)){
- if(identical(FUN_MOD,RunModel_CemaNeigeGR4J)){ FUN1 <- TransfoParam_GR4J; FUN2 <- TransfoParam_CemaNeige; }
- if(identical(FUN_MOD,RunModel_CemaNeigeGR5J)){ FUN1 <- TransfoParam_GR5J; FUN2 <- TransfoParam_CemaNeige; }
- if(identical(FUN_MOD,RunModel_CemaNeigeGR6J)){ FUN1 <- TransfoParam_GR6J; FUN2 <- TransfoParam_CemaNeige; }
- FUN_TRANSFO <- function(ParamIn,Direction){
- Bool <- is.matrix(ParamIn);
- if(Bool==FALSE){ ParamIn <- rbind(ParamIn); }
- ParamOut <- NA*ParamIn;
- NParam <- ncol(ParamIn);
- ParamOut[, 1:(NParam-2)] <- FUN1(ParamIn[, 1:(NParam-2)],Direction);
- ParamOut[,(NParam-1):NParam ] <- FUN2(ParamIn[,(NParam-1):NParam ],Direction);
- if(Bool==FALSE){ ParamOut <- ParamOut[1,]; }
- return(ParamOut);
- }
- }
- if(is.null(FUN_TRANSFO)){ stop("FUN_TRANSFO was not found (in Calibration function) \n"); return(NULL); }
- }
-
-
- ##_RunModelAndCrit
- RunModelAndCrit <- function(par,InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_TRANSFO){
- ParamT <- NA*CalibOptions$FixedParam;
- ParamT[CalibOptions$OptimParam] <- par;
- Param <- FUN_TRANSFO(ParamIn=ParamT,Direction="TR");
- Param[!CalibOptions$OptimParam] <- CalibOptions$FixedParam[!CalibOptions$OptimParam];
- OutputsModel <- FUN_MOD(InputsModel=InputsModel,RunOptions=RunOptions,Param=Param);
- OutputsCrit <- FUN_CRIT(InputsCrit=InputsCrit,OutputsModel=OutputsModel);
- return(OutputsCrit$CritValue*OutputsCrit$Multiplier);
- }
-
-
- ##_temporary_change_of_Outputs_Sim
- RunOptions$Outputs_Sim <- RunOptions$Outputs_Cal; ### this reduces the size of the matrix exchange with fortran and therefore speeds the calibration
- ##_screenPrint
- if(!quiet){
- cat(paste("\t Calibration in progress (function optim from the stats package) \n",sep=""));
- }
-
-
- ##_lower_and_upper_limit_values (transformed)
- RangesR <- CalibOptions$SearchRanges;
- RangesT <- FUN_TRANSFO(RangesR,"RT");
- lower <- RangesT[1,CalibOptions$OptimParam];
- upper <- RangesT[2,CalibOptions$OptimParam];
-
- ##_starting_values (transformed)
- ParamStartT <- FUN_TRANSFO(CalibOptions$StartParam,"RT");
- par_start <- ParamStartT[CalibOptions$OptimParam];
-
-
- ##_calibration
- RESULT <- optim(par=par_start,fn=RunModelAndCrit,gr=NULL,
- InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_TRANSFO, ## arguments for the RunModelAndCrit function (other than par)
- method="L-BFGS-B",lower=lower,upper=upper,control=list(),hessian=FALSE)
-
-
- ##_outputs_preparation
- ParamFinalT <- NA*ParamStartT;
- ParamFinalT[CalibOptions$OptimParam] <- RESULT$par;
- ParamFinalR <- FUN_TRANSFO(ParamFinalT,"TR");
- ParamFinalR[!CalibOptions$OptimParam] <- CalibOptions$FixedParam[!CalibOptions$OptimParam];
- CritFinal <- RESULT$value;
-
- ##_storage_of_crit_info
- OutputsModel <- FUN_MOD(InputsModel=InputsModel,RunOptions=RunOptions,Param=ParamFinalR);
- OutputsCrit <- FUN_CRIT(InputsCrit=InputsCrit,OutputsModel=OutputsModel);
- CritName <- OutputsCrit$CritName;
- CritBestValue <- OutputsCrit$CritBestValue;
- Multiplier <- OutputsCrit$Multiplier;
-
- ##_screenPrint
- if(!quiet){
- if(RESULT$convergence==0){
- cat(paste("\t Calibration completed: \n",sep=""));
- cat(paste("\t Param = ",paste(formatC(ParamFinalR,format="f",width=8,digits=3),collapse=" , "),"\n",sep=""));
- cat(paste("\t Crit ",format(CritName,width=12,justify="left")," = ",formatC(CritFinal*Multiplier,format="f",digits=4),"\n",sep=""));
- } else {
- cat(paste("\t Calibration failed: \n",sep=""));
- cat(paste("\t ",RESULT$message,sep=""));
- }
- }
-
-
- ##_function_output
- OutputsCalib <- list(as.double(ParamFinalR),CritFinal*Multiplier,as.integer(RESULT$counts[1]),CritName,CritBestValue);
- names(OutputsCalib) <- c("ParamFinalR","CritFinal","NRuns","CritName","CritBestValue");
- class(OutputsCalib) <- c("OutputsCalib","optim");
- return(OutputsCalib);
-
-
-}
-
-
-
-
diff --git a/man/Calibration_optim.Rd b/man/Calibration_optim.Rd
deleted file mode 100644
index d24d91b02a0607324eaef9036a5c8b9007e07867..0000000000000000000000000000000000000000
--- a/man/Calibration_optim.Rd
+++ /dev/null
@@ -1,109 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Calibration_optim.R
-\encoding{UTF-8}
-\name{Calibration_optim}
-\alias{Calibration_optim}
-\title{Calibration algorithm which optimises the error criterion selected as objective function using the stats::optim function}
-\usage{
-Calibration_optim(InputsModel, RunOptions, InputsCrit, CalibOptions, FUN_MOD,
- FUN_CRIT, FUN_TRANSFO = NULL, quiet = FALSE)
-}
-\arguments{
-\item{InputsModel}{[object of class \emph{InputsModel}] see \code{\link{CreateInputsModel}} for details}
-
-\item{RunOptions}{[object of class \emph{RunOptions}] see \code{\link{CreateRunOptions}} for details}
-
-\item{InputsCrit}{[object of class \emph{InputsCrit}] see \code{\link{CreateInputsCrit}} for details}
-
-\item{CalibOptions}{[object of class \emph{CalibOptions}] see \code{\link{CreateCalibOptions}} for details}
-
-\item{FUN_MOD}{[function] hydrological model function (e.g. RunModel_GR4J, RunModel_CemaNeigeGR4J)}
-
-\item{FUN_CRIT}{[function] error criterion function (e.g. ErrorCrit_RMSE, ErrorCrit_NSE)}
-
-\item{FUN_TRANSFO}{(optional) [function] model parameters transformation function, if the FUN_MOD used is native in the package, FUN_TRANSFO is automatically defined}
-
-\item{quiet}{(optional) [boolean] boolean indicating if the function is run in quiet mode or not, default=FALSE}
-}
-\value{
-[list] list containing the function outputs organised as follows:
- \tabular{ll}{
- \emph{$ParamFinalR } \tab [numeric] parameter set obtained at the end of the calibration \cr
- \emph{$CritFinal } \tab [numeric] error criterion selected as objective function obtained at the end of the calibration \cr
- \emph{$Nruns } \tab [numeric] number of model runs done during the calibration \cr
- \emph{$CritName } \tab [character] name of the calibration criterion selected as objective function \cr
- \emph{$CritBestValue} \tab [numeric] theoretical best criterion value \cr
- }
-}
-\description{
-Calibration algorithm which optimises the error criterion selected as objective function. \cr
-\cr
-The algorithm is based on the \code{\link{optim}} function from the "stats" R-package
-(using method="L-BFGS-B", i.e. a local optimization quasi-Newton method).
-}
-\details{
-To optimise the exploration of the parameter space, transformation functions are used to convert
-the model parameters. This is done using the TransfoParam functions.
-}
-\examples{
-## loading catchment data
-library(airGR)
-data(L0123001)
-
-## preparation of InputsModel object
-InputsModel <- CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR,
- Precip = BasinObs$P, PotEvap = BasinObs$E)
-
-## calibration period selection
-Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%d/\%m/\%Y \%H:\%M")=="01/01/1990 00:00"),
- which(format(BasinObs$DatesR, format="\%d/\%m/\%Y \%H:\%M")=="31/12/1999 00:00"))
-
-## preparation of RunOptions object
-RunOptions <- CreateRunOptions(FUN_MOD = RunModel_GR4J,
- InputsModel = InputsModel, IndPeriod_Run = Ind_Run)
-
-## calibration criterion: preparation of the InputsCrit object
-InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel,
- RunOptions = RunOptions, Qobs = BasinObs$Qmm[Ind_Run])
-
-## preparation of CalibOptions object
-CalibOptions <- CreateCalibOptions(FUN_MOD = RunModel_GR4J,
- FUN_CALIB = Calibration_optim)
-
-## calibration
-OutputsCalib <- Calibration_optim(InputsModel = InputsModel, RunOptions = RunOptions,
- InputsCrit = InputsCrit, CalibOptions = CalibOptions,
- FUN_MOD = RunModel_GR4J, FUN_CRIT = ErrorCrit_NSE)
-
-## simulation
-Param <- OutputsCalib$ParamFinalR
-OutputsModel <- RunModel_GR4J(InputsModel = InputsModel,
- RunOptions = RunOptions, Param = Param)
-
-## results preview
-plot_OutputsModel(OutputsModel = OutputsModel, Qobs = BasinObs$Qmm[Ind_Run])
-
-## efficiency criterion: Nash-Sutcliffe Efficiency
-InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel,
- RunOptions = RunOptions, Qobs = BasinObs$Qmm[Ind_Run])
-OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
-cat(paste(" Crit ", OutputsCrit$CritName, " ",
- round(OutputsCrit$CritValue, 4), "\\n", sep = ""))
-
-## efficiency criterion: Kling-Gupta Efficiency
-InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_KGE, InputsModel = InputsModel,
- RunOptions = RunOptions, Qobs = BasinObs$Qmm[Ind_Run])
-OutputsCrit <- ErrorCrit_KGE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
-cat(paste(" Crit ", OutputsCrit$CritName, " ",
- round(OutputsCrit$CritValue, 4), "\\n", sep = ""))
-}
-\author{
-Laurent Coron (August 2013)
-}
-\seealso{
-\code{\link{Calibration}}, \code{\link{Calibration_Michel}},
- \code{\link{RunModel_GR4J}}, \code{\link{TransfoParam_GR4J}}, \code{\link{ErrorCrit_RMSE}},
- \code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}},
- \code{\link{CreateInputsCrit}}, \code{\link{CreateCalibOptions}}.
-}
-