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Commit 58419018 authored by Delaigue Olivier's avatar Delaigue Olivier
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Signed-off-by: Delaigue Olivier's avatarOlivier Delaigue <olivier.delaigue@irstea.fr>
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^.*\.Rproj$
^\.Rproj\.user$
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.Rproj.user
.Rhistory
.RData
src/*.o
src/*.so
src/*.dll
DESCRIPTION deleted 100644 → 0
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Package: airGR
Type: Package
Title: Modelling tools used at Irstea-HBAN (France), including GR4J,
GR5J, GR6J and CemaNeige
Version: 0.7.4
Date: 2014-11-01
Author: Laurent CORON
Maintainer: Laurent CORON <laurent.coron@irstea.fr>, Olivier DELAIGUE
<olivier.delaigue@irstea.fr>
Depends: R (>= 3.0.1)
Description: This package brings into R the hydrological modelling tools used
at Irstea-HBAN (France). The package includes several conceptual
rainfall-runoff models and the associated functions for their calibration
and evaluation,including GR4J, GR5J, GR6J and CemaNeige. Use help(airGR)
for package description.
License: GPL-2
Packaged: 2014-11-25 21:51:31 UTC; H61970
NAMESPACE deleted 100644 → 0
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# Generated by roxygen2 (4.0.1): do not edit by hand
export(Calibration)
export(Calibration_HBAN)
export(Calibration_optim)
export(CreateCalibOptions)
export(CreateInputsCrit)
export(CreateInputsModel)
export(CreateRunOptions)
export(DataAltiExtrapolation_HBAN)
export(ErrorCrit)
export(ErrorCrit_KGE)
export(ErrorCrit_KGE2)
export(ErrorCrit_NSE)
export(ErrorCrit_RMSE)
export(PEdaily_Oudin)
export(RunModel)
export(RunModel_CemaNeige)
export(RunModel_CemaNeigeGR4J)
export(RunModel_CemaNeigeGR5J)
export(RunModel_CemaNeigeGR6J)
export(RunModel_GR4J)
export(RunModel_GR5J)
export(RunModel_GR6J)
export(TransfoParam)
export(TransfoParam_CemaNeige)
export(TransfoParam_GR4J)
export(TransfoParam_GR5J)
export(TransfoParam_GR6J)
export(plot_OutputsModel)
useDynLib(airgr)
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#' @name BasinInfo
#' @docType data
#' @title Data sample: characteristics of a fictional catchment (L0123001, L0123002 or L0123003)
#' @description
#' R-object containing the code, station's name, area and hypsometric curve of the catchment.
#' @encoding UTF-8
#' @format
#' List named 'BasinInfo' containing
#' \itemize{
#' \item two strings: catchment's code and station's name
#' \item one float: catchment's area in km2
#' \item one numeric vector: catchment's hypsometric curve (min, quantiles 01 to 99 and max) in metres
#' }
#' @examples
#' require(airGR)
#' data(L0123001)
#' str(BasinInfo)
NULL
#' @name BasinObs
#' @docType data
#' @title Data sample: time series of observations of a fictional catchment (L0123001, L0123002 or L0123003)
#' @description
#' R-object containing the times series of precipitation, temperature, potential evapotranspiration and discharges. \cr
#' Times series for L0123001 or L0123002 are at the daily time-step for use with daily models such as GR4J, GR5J, GR6J, CemaNeigeGR4J, CemaNeigeGR5J and CemaNeigeGR6J.
#' Times series for L0123003 are at the hourly time-step for use with hourly models such as GR4H.
#' @encoding UTF-8
#' @format
#' Data frame named 'BasinObs' containing
#' \itemize{
#' \item one POSIXlt vector: time series dates in the POSIXlt format
#' \item five numeric vectors: time series of catchment average precipitation [mm], catchment average air temperature [degC], catchment average potential evapotranspiration [mm], outlet discharge [l/s], outlet discharge [mm]
#' }
#' @examples
#' require(airGR)
#' data(L0123001)
#' str(BasinObs)
NULL
R/Calibration.R deleted 100644 → 0
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#*************************************************************************************************
#' Calibration algorithm which minimises the error criterion using the provided functions. \cr
#*************************************************************************************************
#' @title Calibration algorithm which minimises an error criterion on the model outputs using the provided functions
#' @author Laurent Coron (June 2014)
#' @seealso \code{\link{Calibration_HBAN}}, \code{\link{Calibration_optim}},
#' \code{\link{RunModel}}, \code{\link{ErrorCrit}}, \code{\link{TransfoParam}},
#' \code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}},
#' \code{\link{CreateInputsCrit}}, \code{\link{CreateCalibOptions}}.
#' @example tests/example_Calibration.R
#' @export
#' @encoding UTF-8
#_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_CALIB (optional) [function] calibration algorithm function (e.g. Calibration_HBAN, Calibration_optim), default=Calibration_HBAN
#' @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] see \code{\link{Calibration_HBAN}} or \code{\link{Calibration_optim}}
#**************************************************************************************************
Calibration <- function(InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_CALIB=Calibration_HBAN,FUN_TRANSFO=NULL,quiet=FALSE){
return( FUN_CALIB(InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_TRANSFO,quiet=quiet) )
}
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R/Calibration_optim.R deleted 100644 → 0
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#*************************************************************************************************
#' 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_HBAN}},
#' \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_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_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)
}
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#*************************************************************************************************
#' Creation of the CalibOptions object required to the Calibration functions.
#'
#' Users wanting to use FUN_MOD, FUN_CALIB or FUN_TRANSFO functions that are not included in
#' the package must create their own CalibOptions object accordingly.
#*************************************************************************************************
#' @title Creation of the CalibOptions object required to the Calibration functions
#' @author Laurent Coron (June 2014)
#' @seealso \code{\link{RunModel}}, \code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}}, \code{\link{CreateInputsCrit}}
#' @example tests/example_Calibration.R
#' @encoding UTF-8
#' @export
#_FunctionInputs__________________________________________________________________________________
#' @param FUN_MOD [function] hydrological model function (e.g. RunModel_GR4J, RunModel_CemaNeigeGR4J)
#' @param FUN_CALIB (optional) [function] calibration algorithm function (e.g. Calibration_HBAN, Calibration_optim), default=Calibration_HBAN
#' @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 RunOptions (optional) [object of class \emph{RunOptions}] see \code{\link{CreateRunOptions}} for details
#' @param OptimParam (optional) [boolean] vector of booleans indicating which parameters must be optimised (NParam columns, 1 line)
#' @param FixedParam (optional) [numeric] vector giving the values to allocate to non-optimised parameter values (NParam columns, 1 line)
#' @param SearchRanges (optional) [numeric] matrix giving the ranges of real parameters (NParam columns, 2 lines)
#' \tabular{llllll}{
#' \tab [X1] \tab [X2] \tab [X3] \tab [...] \tab [Xi] \cr
#' [1,] \tab 0 \tab -1 \tab 0 \tab ... \tab 0.0 \cr
#' [2,] \tab 3000 \tab +1 \tab 100 \tab ... \tab 3.0 \cr
#' }
#' @param StartParam (optional) [numeric] vector of parameter values used to start global search calibration procedure (e.g. Calibration_optim)
#' \tabular{llllll}{
#' \tab [X1] \tab [X2] \tab [X3] \tab [...] \tab [Xi] \cr
#' \tab 1000 \tab -0.5 \tab 22 \tab ... \tab 1.1 \cr
#' }
#' @param StartParamList (optional) [numeric] matrix of parameter sets used for grid-screening calibration procedure (values in columns, sets in line)
#' \tabular{llllll}{
#' \tab [X1] \tab [X2] \tab [X3] \tab [...] \tab [Xi] \cr
#' [set1] \tab 800 \tab -0.7 \tab 25 \tab ... \tab 1.0 \cr
#' [set2] \tab 1000 \tab -0.5 \tab 22 \tab ... \tab 1.1 \cr
#' [...] \tab ... \tab ... \tab ... \tab ... \tab ... \cr
#' [set n] \tab 200 \tab -0.3 \tab 17 \tab ... \tab 1.0 \cr
#' }
#' @param StartParamDistrib (optional) [numeric] matrix of parameter values used for grid-screening calibration procedure (values in columns, percentiles in line) \cr
#' \tabular{llllll}{
#' \tab [X1] \tab [X2] \tab [X3] \tab [...] \tab [Xi] \cr
#' [value1] \tab 800 \tab -0.7 \tab 25 \tab ... \tab 1.0 \cr
#' [value2] \tab 1000 \tab NA \tab 50 \tab ... \tab 1.2 \cr
#' [value3] \tab 1200 \tab NA \tab NA \tab ... \tab 1.6 \cr
#' }
#_FunctionOutputs_________________________________________________________________________________
#' @return [list] object of class \emph{CalibOptions} containing the data required to evaluate the model outputs; it can include the following:
#' \tabular{ll}{
#' \emph{$OptimParam } \tab [boolean] vector of booleans indicating which parameters must be optimised \cr
#' \emph{$FixedParam } \tab [numeric] vector giving the values to allocate to non-optimised parameter values \cr
#' \emph{$SearchRanges } \tab [numeric] matrix giving the ranges of real parameters \cr
#' \emph{$StartParam } \tab [numeric] vector of parameter values used to start global search calibration procedure \cr
#' \emph{$StartParamList } \tab [numeric] matrix of parameter sets used for grid-screening calibration procedure \cr
#' \emph{$StartParamDistrib} \tab [numeric] matrix of parameter values used for grid-screening calibration procedure \cr
#' }
#**************************************************************************************************'
CreateCalibOptions <- function(FUN_MOD,FUN_CALIB=Calibration_HBAN,FUN_TRANSFO=NULL,RunOptions=NULL,OptimParam=NULL,FixedParam=NULL,SearchRanges=NULL,
StartParam=NULL,StartParamList=NULL,StartParamDistrib=NULL){
ObjectClass <- NULL;
##check_FUN_MOD
BOOL <- FALSE;
if(identical(FUN_MOD,RunModel_GR4J )){ ObjectClass <- c(ObjectClass,"GR4J" ); BOOL <- TRUE; }
if(identical(FUN_MOD,RunModel_GR5J )){ ObjectClass <- c(ObjectClass,"GR5J" ); BOOL <- TRUE; }
if(identical(FUN_MOD,RunModel_GR6J )){ ObjectClass <- c(ObjectClass,"GR6J" ); BOOL <- TRUE; }
if(identical(FUN_MOD,RunModel_CemaNeige )){ ObjectClass <- c(ObjectClass,"CemaNeige" ); BOOL <- TRUE; }
if(identical(FUN_MOD,RunModel_CemaNeigeGR4J)){ ObjectClass <- c(ObjectClass,"CemaNeigeGR4J"); BOOL <- TRUE; }
if(identical(FUN_MOD,RunModel_CemaNeigeGR5J)){ ObjectClass <- c(ObjectClass,"CemaNeigeGR5J"); BOOL <- TRUE; }
if(identical(FUN_MOD,RunModel_CemaNeigeGR6J)){ ObjectClass <- c(ObjectClass,"CemaNeigeGR6J"); BOOL <- TRUE; }
if(!BOOL){ stop("incorrect FUN_MOD for use in CreateCalibOptions \n"); return(NULL); }
##check_FUN_CALIB
BOOL <- FALSE;
if(identical(FUN_CALIB,Calibration_HBAN )){ ObjectClass <- c(ObjectClass,"HBAN" ); BOOL <- TRUE; }
if(identical(FUN_CALIB,Calibration_optim)){ ObjectClass <- c(ObjectClass,"optim"); BOOL <- TRUE; }
if(!BOOL){ stop("incorrect FUN_CALIB for use in CreateCalibOptions \n"); return(NULL); }
##check_FUN_TRANSFO
if(is.null(FUN_TRANSFO)){
##_set_FUN1
if(identical(FUN_MOD,RunModel_GR4J ) | identical(FUN_MOD,RunModel_CemaNeigeGR4J) ){ FUN1 <- TransfoParam_GR4J ; }
if(identical(FUN_MOD,RunModel_GR5J ) | identical(FUN_MOD,RunModel_CemaNeigeGR5J) ){ FUN1 <- TransfoParam_GR5J ; }
if(identical(FUN_MOD,RunModel_GR6J ) | identical(FUN_MOD,RunModel_CemaNeigeGR6J) ){ FUN1 <- TransfoParam_GR6J ; }
if(identical(FUN_MOD,RunModel_CemaNeige) ){ FUN1 <- TransfoParam_CemaNeige; }
if(is.null(FUN1)){ stop("FUN1 was not found \n"); return(NULL); }
##_set_FUN2
FUN2 <- TransfoParam_CemaNeige;
##_set_FUN_TRANSFO
if(identical(FUN_MOD,RunModel_GR4J) | identical(FUN_MOD,RunModel_GR5J) | identical(FUN_MOD,RunModel_GR6J) | identical(FUN_MOD,RunModel_CemaNeige)){
FUN_TRANSFO <- FUN1;
} else {
FUN_TRANSFO <- function(ParamIn,Direction){
Bool <- is.matrix(ParamIn);
if(Bool==FALSE){ ParamIn <- rbind(ParamIn); }
ParamOut <- NA*ParamIn;
NParam <- ncol(ParamIn);
if(NParam <= 3){
ParamOut[, 1:(NParam-2)] <- FUN1(cbind(ParamIn[,1:(NParam-2)]),Direction);
} else {
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 \n"); return(NULL); }
##check_RunOptions
if(!is.null(RunOptions)){
if(inherits(RunOptions,"RunOptions")==FALSE){ stop("RunOptions must be of class 'RunOptions' if not null= \n"); return(NULL); }
}
##NParam
if("GR4J" %in% ObjectClass){ NParam <- 4; }
if("GR5J" %in% ObjectClass){ NParam <- 5; }
if("GR6J" %in% ObjectClass){ NParam <- 6; }
if("CemaNeige" %in% ObjectClass){ NParam <- 2; }
if("CemaNeigeGR4J" %in% ObjectClass){ NParam <- 6; }
if("CemaNeigeGR5J" %in% ObjectClass){ NParam <- 7; }
if("CemaNeigeGR6J" %in% ObjectClass){ NParam <- 8; }
##check_OptimParam
if(is.null(OptimParam)){
OptimParam <- rep(TRUE,NParam);
} else {
if(!is.vector(OptimParam) ){ stop("OptimParam must be a vector of booleans \n"); return(NULL); }
if(length(OptimParam)!=NParam){ stop("Incompatibility between OptimParam length and FUN_MOD \n"); return(NULL); }
if(!is.logical(OptimParam) ){ stop("OptimParam must be a vector of booleans \n"); return(NULL); }
}
##check_FixedParam
if(is.null(FixedParam)){
FixedParam <- rep(NA,NParam);
} else {
if(!is.vector(FixedParam) ){ stop("FixedParam must be a vector \n"); return(NULL); }
if(length(FixedParam)!=NParam ){ stop("Incompatibility between OptimParam length and FUN_MOD \n"); return(NULL); }
if(!is.numeric(FixedParam[!OptimParam])){ stop("if OptimParam[i]==FALSE, FixedParam[i] must be a numeric value \n"); return(NULL); }
}
##check_SearchRanges
if(is.null(SearchRanges)){
ParamT <- matrix(c(rep(-9.99,NParam),rep(+9.99,NParam)),ncol=NParam,byrow=TRUE);
SearchRanges <- TransfoParam(ParamIn=ParamT,Direction="TR",FUN_TRANSFO=FUN_TRANSFO);
} else {
if(!is.matrix( SearchRanges) ){ stop("SearchRanges must be a matrix \n"); return(NULL); }
if(!is.numeric(SearchRanges) ){ stop("SearchRanges must be a matrix of numeric values \n"); return(NULL); }
if(sum(is.na(SearchRanges))!=0){ stop("SearchRanges must not include NA values \n"); return(NULL); }
if(nrow(SearchRanges)!=2 ){ stop("SearchRanges must have 2 rows \n"); return(NULL); }
if(ncol(SearchRanges)!=NParam ){ stop("Incompatibility between SearchRanges ncol and FUN_MOD \n"); return(NULL); }
}
##check_StartParamList_and_StartParamDistrib__default_values
if( ("HBAN" %in% ObjectClass & is.null(StartParamList) & is.null(StartParamDistrib)) |
("optim" %in% ObjectClass & is.null(StartParam)) ){
if("GR4J"%in% ObjectClass){
ParamT <- matrix( c( +3.60, -2.00, +3.40, -9.10,
+3.90, -0.90, +4.10, -8.70,
+4.50, -0.10, +5.00, -8.10),ncol=NParam,byrow=TRUE); }
if("GR5J"%in% ObjectClass){
ParamT <- matrix( c( +3.60, -1.70, +3.30, -9.10, -0.70,
+3.90, -0.60, +4.10, -8.70, +0.30,
+4.50, -0.10, +5.00, -8.10, +0.50),ncol=NParam,byrow=TRUE); }
if("GR6J"%in% ObjectClass){
ParamT <- matrix( c( +3.60, -1.00, +3.30, -9.10, -0.90, +3.00,
+3.90, -0.50, +4.10, -8.70, +0.10, +4.00,
+4.50, +0.50, +5.00, -8.10, +1.10, +5.00),ncol=NParam,byrow=TRUE); }
if("CemaNeige"%in% ObjectClass){
ParamT <- matrix( c( -6.26, +0.55,
-2.13, +0.92,
+4.86, +1.40),ncol=NParam,byrow=TRUE); }
if("CemaNeigeGR4J"%in% ObjectClass){
ParamT <- matrix( c( +3.60, -2.00, +3.40, -9.10, -6.26, +0.55,
+3.90, -0.90, +4.10, -8.70, -2.13, +0.92,
+4.50, -0.10, +5.00, -8.10, +4.86, +1.40),ncol=NParam,byrow=TRUE); }
if("CemaNeigeGR5J"%in% ObjectClass){
ParamT <- matrix( c( +3.60, -1.70, +3.30, -9.10, -0.70, -6.26, +0.55,
+3.90, -0.60, +4.10, -8.70, +0.30, -2.13, +0.92,
+4.50, -0.10, +5.00, -8.10, +0.50, +4.86, +1.40),ncol=NParam,byrow=TRUE); }
if("CemaNeigeGR6J"%in% ObjectClass){
ParamT <- matrix( c( +3.60, -1.00, +3.30, -9.10, -0.90, +3.00, -6.26, +0.55,
+3.90, -0.50, +4.10, -8.70, +0.10, +4.00, -2.13, +0.92,
+4.50, +0.50, +5.00, -8.10, +1.10, +5.00, +4.86, +1.40),ncol=NParam,byrow=TRUE); }
StartParamList <- NULL;
StartParamDistrib <- TransfoParam(ParamIn=ParamT,Direction="TR",FUN_TRANSFO=FUN_TRANSFO);
StartParam <- StartParamDistrib[2,];
}
##check_StartParamList_and_StartParamDistrib__format
if("HBAN" %in% ObjectClass & !is.null(StartParamList)){
if(!is.matrix( StartParamList) ){ stop("StartParamList must be a matrix \n"); return(NULL); }
if(!is.numeric(StartParamList) ){ stop("StartParamList must be a matrix of numeric values \n"); return(NULL); }
if(sum(is.na(StartParamList))!=0){ stop("StartParamList must not include NA values \n"); return(NULL); }
if(ncol(StartParamList)!=NParam ){ stop("Incompatibility between StartParamList ncol and FUN_MOD \n"); return(NULL); }
}
if("HBAN" %in% ObjectClass & !is.null(StartParamDistrib)){
if(!is.matrix( StartParamDistrib) ){ stop("StartParamDistrib must be a matrix \n"); return(NULL); }
if(!is.numeric(StartParamDistrib[1,]) ){ stop("StartParamDistrib must be a matrix of numeric values \n"); return(NULL); }
if(sum(is.na(StartParamDistrib[1,]))!=0){ stop("StartParamDistrib must not include NA values on the first line \n"); return(NULL); }
if(ncol(StartParamDistrib)!=NParam ){ stop("Incompatibility between StartParamDistrib ncol and FUN_MOD \n"); return(NULL); }
}
if("optim" %in% ObjectClass & !is.null(StartParam)){
if(!is.vector( StartParam) ){ stop("StartParam must be a vector \n"); return(NULL); }
if(!is.numeric(StartParam) ){ stop("StartParam must be a vector of numeric values \n"); return(NULL); }
if(sum(is.na(StartParam))!=0 ){ stop("StartParam must not include NA values \n"); return(NULL); }
if(length(StartParam)!=NParam ){ stop("Incompatibility between StartParam length and FUN_MOD \n"); return(NULL); }
}
##Create_CalibOptions
CalibOptions <- list(OptimParam=OptimParam,FixedParam=FixedParam,SearchRanges=SearchRanges);
if(!is.null(StartParam )){ CalibOptions <- c(CalibOptions,list(StartParam=StartParam)); }
if(!is.null(StartParamList )){ CalibOptions <- c(CalibOptions,list(StartParamList=StartParamList)); }
if(!is.null(StartParamDistrib)){ CalibOptions <- c(CalibOptions,list(StartParamDistrib=StartParamDistrib)); }
class(CalibOptions) <- c("CalibOptions",ObjectClass);
return(CalibOptions);
}
R/CreateInputsCrit.R deleted 100644 → 0
View file @ c3ad2525
#*************************************************************************************************
#' Creation of the InputsCrit object required to the ErrorCrit functions.
#'
#' Users wanting to use FUN_CRIT functions that are not included in
#' the package must create their own InputsCrit object accordingly.
#*************************************************************************************************
#' @title Creation of the InputsCrit object required to the ErrorCrit functions
#' @author Laurent Coron (June 2014)
#' @seealso \code{\link{RunModel}}, \code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}}, \code{\link{CreateCalibOptions}}
#' @example tests/example_ErrorCrit.R
#' @encoding UTF-8
#' @export
#_FunctionInputs__________________________________________________________________________________
#' @param FUN_CRIT [function] error criterion function (e.g. ErrorCrit_RMSE, ErrorCrit_NSE)
#' @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 Qobs [numeric] series of observed discharges [mm]
#' @param BoolCrit (optional) [boolean] boolean giving the time steps to consider in the computation (all time steps are consider by default)
#' @param transfo (optional) [character] name of the transformation (e.g. "", "sqrt", "log", "inv", "sort")
#' @param Ind_zeroes (optional) [numeric] indices of the time-steps where zeroes are observed
#' @param epsilon (optional) [numeric] epsilon to add to all Qobs and Qsim if \emph{$Ind_zeroes} is not empty
#_FunctionOutputs_________________________________________________________________________________
#' @return [list] object of class \emph{InputsCrit} containing the data required to evaluate the model outputs; it can include the following:
#' \tabular{ll}{
#' \emph{$BoolCrit } \tab [boolean] boolean giving the time steps to consider in the computation \cr
#' \emph{$Qobs } \tab [numeric] series of observed discharges [mm] \cr
#' \emph{$transfo } \tab [character] name of the transformation (e.g. "", "sqrt", "log", "inv", "sort") \cr
#' \emph{$Ind_zeroes} \tab [numeric] indices of the time-steps where zeroes are observed \cr
#' \emph{$epsilon } \tab [numeric] epsilon to add to all Qobs and Qsim if \emph{$Ind_zeroes} is not empty \cr
#' }
#**************************************************************************************************
CreateInputsCrit <- function(FUN_CRIT,InputsModel,RunOptions,Qobs,BoolCrit=NULL,transfo="",Ind_zeroes=NULL,epsilon=NULL){
ObjectClass <- NULL;
##check_FUN_CRIT
BOOL <- FALSE;
if(identical(FUN_CRIT,ErrorCrit_RMSE) | identical(FUN_CRIT,ErrorCrit_NSE) | identical(FUN_CRIT,ErrorCrit_KGE) | identical(FUN_CRIT,ErrorCrit_KGE2)){
BOOL <- TRUE;
}
if(!BOOL){ stop("incorrect FUN_CRIT for use in CreateInputsCrit \n"); return(NULL); }
##check_arguments
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); }
LLL <- length(InputsModel$DatesR[RunOptions$IndPeriod_Run])
if(is.null(Qobs) ){ stop("Qobs is missing \n"); return(NULL); }
if(!is.vector( Qobs)){ stop(paste("Qobs must be a vector of numeric values \n",sep="")); return(NULL); }
if(!is.numeric(Qobs)){ stop(paste("Qobs must be a vector of numeric values \n",sep="")); return(NULL); }
if(length(Qobs)!=LLL){ stop("Qobs and InputsModel series must have the same length \n"); return(NULL); }
if(is.null(BoolCrit)){ BoolCrit <- rep(TRUE,length(Qobs)); }
if(!is.logical(BoolCrit)){ stop("BoolCrit must be a vector of boolean \n" ); return(NULL); }
if(length(BoolCrit)!=LLL){ stop("BoolCrit and InputsModel series must have the same length \n"); return(NULL); }
if(is.null(transfo) ){ stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' \n"); return(NULL); }
if(!is.vector( transfo)){ stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' \n"); return(NULL); }
if(length(transfo)!=1 ){ stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' \n"); return(NULL); }
if(!is.character(transfo)){ stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' \n"); return(NULL); }
if(transfo %in% c("","sqrt","log","inv") == FALSE){
stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' \n"); return(NULL); }