From eb3f809f86414c791f7624710dbe4004d1dc4a80 Mon Sep 17 00:00:00 2001
From: Olivier Delaigue <olivier.delaigue@irstea.fr>
Date: Thu, 14 Apr 2016 15:59:04 +0200
Subject: [PATCH] Renommage des fonctions avec le suffixe HBAN
---
...alibration_HBAN.R => Calibration_Michel.R} | 8 +-
..._HBAN.R => DataAltiExtrapolation_Valery.R} | 2 +-
man/Calibration_HBAN.Rd | 128 -----------------
man/Calibration_Michel.Rd | 130 ++++++++++++++++++
...BAN.Rd => DataAltiExtrapolation_Valery.Rd} | 12 +-
...on_HBAN.R => example_Calibration_Michel.R} | 4 +-
6 files changed, 143 insertions(+), 141 deletions(-)
rename R/{Calibration_HBAN.R => Calibration_Michel.R} (98%)
rename R/{DataAltiExtrapolation_HBAN.R => DataAltiExtrapolation_Valery.R} (99%)
delete mode 100644 man/Calibration_HBAN.Rd
create mode 100644 man/Calibration_Michel.Rd
rename man/{DataAltiExtrapolation_HBAN.Rd => DataAltiExtrapolation_Valery.Rd} (91%)
rename tests/{example_Calibration_HBAN.R => example_Calibration_Michel.R} (95%)
diff --git a/R/Calibration_HBAN.R b/R/Calibration_Michel.R
similarity index 98%
rename from R/Calibration_HBAN.R
rename to R/Calibration_Michel.R
index 152ac7a5..20600c56 100644
--- a/R/Calibration_HBAN.R
+++ b/R/Calibration_Michel.R
@@ -27,7 +27,7 @@
#' @references
#' Michel, C. (1991),
#' Hydrologie appliquée aux petits bassins ruraux, Hydrology handout (in French), Cemagref, Antony, France.
-#' @example tests/example_Calibration_HBAN.R
+#' @example tests/example_Calibration_Michel.R
#' @seealso \code{\link{Calibration}}, \code{\link{Calibration_optim}},
#' \code{\link{RunModel_GR4J}}, \code{\link{TransfoParam_GR4J}}, \code{\link{ErrorCrit_RMSE}},
#' \code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}},
@@ -57,7 +57,7 @@
#' \emph{$CritBestValue} \tab [numeric] theoretical best criterion value \cr
#' }
#**************************************************************************************************
-Calibration_HBAN <- function(InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_TRANSFO=NULL,quiet=FALSE){
+Calibration_Michel <- function(InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_TRANSFO=NULL,quiet=FALSE){
##_____Arguments_check_____________________________________________________________________
@@ -65,7 +65,7 @@ Calibration_HBAN <- function(InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_
if(inherits(RunOptions,"RunOptions")==FALSE){ stop("RunOptions must be of class 'RunOptions' \n"); return(NULL); }
if(inherits(InputsCrit,"InputsCrit")==FALSE){ stop("InputsCrit must be of class 'InputsCrit' \n"); return(NULL); }
if(inherits(CalibOptions,"CalibOptions")==FALSE){ stop("CalibOptions must be of class 'CalibOptions' \n"); return(NULL); }
- if(inherits(CalibOptions,"HBAN")==FALSE){ stop("CalibOptions must be of class 'HBAN' if Calibration_HBAN is used \n"); return(NULL); }
+ if(inherits(CalibOptions,"HBAN")==FALSE){ stop("CalibOptions must be of class 'HBAN' if Calibration_Michel is used \n"); return(NULL); }
##_check_FUN_TRANSFO
@@ -101,7 +101,7 @@ Calibration_HBAN <- function(InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_
if("StartParamDistrib" %in% names(CalibOptions)){ PrefilteringType <- 2; } else { PrefilteringType <- 1; }
if(PrefilteringType==1){ NParam <- ncol(CalibOptions$StartParamList); }
if(PrefilteringType==2){ NParam <- ncol(CalibOptions$StartParamDistrib); }
- if(NParam>20){ stop("Calibration_HBAN can handle a maximum of 20 parameters \n"); return(NULL); }
+ if(NParam>20){ stop("Calibration_Michel can handle a maximum of 20 parameters \n"); return(NULL); }
HistParamR <- matrix(NA,nrow=500*NParam,ncol=NParam);
HistParamT <- matrix(NA,nrow=500*NParam,ncol=NParam);
HistCrit <- matrix(NA,nrow=500*NParam,ncol=1);
diff --git a/R/DataAltiExtrapolation_HBAN.R b/R/DataAltiExtrapolation_Valery.R
similarity index 99%
rename from R/DataAltiExtrapolation_HBAN.R
rename to R/DataAltiExtrapolation_Valery.R
index 7a5354b6..8b001bb1 100644
--- a/R/DataAltiExtrapolation_HBAN.R
+++ b/R/DataAltiExtrapolation_Valery.R
@@ -40,7 +40,7 @@
#' \emph{$ZLayers } \tab [numeric] vector of median elevation for each layer \cr
#' }
#*****************************************************************************************************************
-DataAltiExtrapolation_HBAN <- function(DatesR,Precip,TempMean,TempMin=NULL,TempMax=NULL,ZInputs,HypsoData,NLayers,quiet=FALSE){
+DataAltiExtrapolation_Valery <- function(DatesR,Precip,TempMean,TempMin=NULL,TempMax=NULL,ZInputs,HypsoData,NLayers,quiet=FALSE){
##Altitudinal_gradient_functions_______________________________________________________________
diff --git a/man/Calibration_HBAN.Rd b/man/Calibration_HBAN.Rd
deleted file mode 100644
index 924f74cf..00000000
--- a/man/Calibration_HBAN.Rd
+++ /dev/null
@@ -1,128 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Calibration_HBAN.R
-\encoding{UTF-8}
-\name{Calibration_HBAN}
-\alias{Calibration_HBAN}
-\title{Calibration algorithm which minimises the error criterion using the Irstea-HBAN procedure}
-\usage{
-Calibration_HBAN(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 obtained at the end of the calibration \cr
- \emph{$NIter } \tab [numeric] number of iterations during the calibration \cr
- \emph{$NRuns } \tab [numeric] number of model runs done during the calibration \cr
- \emph{$HistParamR } \tab [numeric] table showing the progression steps in the search for optimal set: parameter values \cr
- \emph{$HistCrit } \tab [numeric] table showing the progression steps in the search for optimal set: criterion values \cr
- \emph{$MatBoolCrit } \tab [boolean] table giving the requested and actual time steps when the model is calibrated \cr
- \emph{$CritName } \tab [character] name of the calibration criterion \cr
- \emph{$CritBestValue} \tab [numeric] theoretical best criterion value \cr
- }
-}
-\description{
-Calibration algorithm which minimises the error criterion. \cr
-\cr
-The algorithm is based on a local search procedure.
-First, a screening is performed using either a rough predefined grid or a list of parameter sets
-and then a simple steepest descent local search algorithm is performed.
-}
-\details{
-A screening is first performed either from a rough predefined grid (considering various initial
-values for each paramete) or from a list of initial parameter sets. \cr
-The best set identified in this screening is then used as a starting point for the steepest
-descent local search algorithm. \cr
-For this search, the parameters are used in a transformed version, to obtain uniform
-variation ranges (and thus a similar pace), while the true ranges might be quite different. \cr
-At each iteration, we start from a parameter set of NParam values (NParam being the number of
-free parameters of the chosen hydrological model) and we determine the 2*NParam-1 new candidates
-by changing one by one the different parameters (+/- pace). \cr
-All these candidates are tested and the best one kept to be the starting point for the next
-iteration. At the end of each iteration, the pace is either increased or decreased to adapt
-the progression speed. A diagonal progress can occasionally be done. \cr
-The calibration algorithm stops when the pace becomes too small. \cr
-
-To optimise the exploration of the parameter space, transformation functions are used to convert
-the model parameters. This is done using the TransfoParam functions.
-}
-\examples{
-## load of catchment data
-require(airGR)
-data(L0123001)
-
-## preparation of InputsModel object
-InputsModel <- CreateInputsModel(FUN_MOD=RunModel_GR4J,DatesR=BasinObs$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$Qmm[Ind_Run])
-
-## preparation of CalibOptions object
-CalibOptions <- CreateCalibOptions(FUN_MOD=RunModel_GR4J,FUN_CALIB=Calibration_HBAN)
-
-## calibration
-OutputsCalib <- Calibration_HBAN(InputsModel=InputsModel,RunOptions=RunOptions,
- InputsCrit=InputsCrit,CalibOptions=CalibOptions,
- FUN_MOD=RunModel_GR4J,FUN_CRIT=ErrorCrit_NSE)
-
-## simulation
-Param <- OutputsCalib$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)
-}
-\references{
-Michel, C. (1991),
- Hydrologie appliquée aux petits bassins ruraux, Hydrology handout (in French), Cemagref, Antony, France.
-}
-\seealso{
-\code{\link{Calibration}}, \code{\link{Calibration_optim}},
- \code{\link{RunModel_GR4J}}, \code{\link{TransfoParam_GR4J}}, \code{\link{ErrorCrit_RMSE}},
- \code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}},
- \code{\link{CreateInputsCrit}}, \code{\link{CreateCalibOptions}}.
-}
-
diff --git a/man/Calibration_Michel.Rd b/man/Calibration_Michel.Rd
new file mode 100644
index 00000000..8a576b1f
--- /dev/null
+++ b/man/Calibration_Michel.Rd
@@ -0,0 +1,130 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Calibration_Michel.R
+\encoding{UTF-8}
+\name{Calibration_Michel}
+\alias{Calibration_Michel}
+\title{Calibration algorithm optimises the error criterion selected as objective function using the Irstea-HBAN procedure described by C. Michel}
+\usage{
+Calibration_Michel(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{$CritFinal } \tab [numeric] error criterion selected as objective function obtained at the end of the calibration \cr
+ \emph{$NIter } \tab [numeric] number of iterations during the calibration \cr
+ \emph{$NRuns } \tab [numeric] number of model runs done during the calibration \cr
+ \emph{$HistParamR } \tab [numeric] table showing the progression steps in the search for optimal set: parameter values \cr
+ \emph{$HistCrit } \tab [numeric] table showing the progression steps in the search for optimal set: criterion values \cr
+ \emph{$MatBoolCrit } \tab [boolean] table giving the requested and actual time steps over which the model is calibrated \cr
+ \emph{$CritName } \tab [character] name of the calibration criterion used as objective function \cr
+ \emph{$CritBestValue} \tab [numeric] theoretical best criterion value \cr
+ }
+}
+\description{
+Calibration algorithm optimises the error criterion selected as objective function. \cr
+\cr
+The algorithm is based on a local search procedure.
+First, a screening is performed using either a rough predefined grid or a list of parameter sets
+and then a simple steepest descent local search algorithm is performed.
+}
+\details{
+A screening is first performed either based on a rough predefined grid (considering various initial
+values for each parameter) or from a list of initial parameter sets. \cr
+The best set identified in this screening is then used as a starting point for the steepest
+descent local search algorithm. \cr
+For this search, since the ranges of parameter values can be quite different,
+simple mathematical transformations are applied to parameters to make them vary
+in a similar range and get a similar sensitivity to a predefined search step. This is done using the TransfoParam functions. \cr
+During the steepest descent method, at each iteration, we start from a parameter set of NParam values (NParam being the number of
+free parameters of the chosen hydrological model) and we determine the 2*NParam-1 new candidates
+by changing one by one the different parameters (+/- search step). \cr
+All these candidates are tested and the best one kept to be the starting point for the next
+iteration. At the end of each iteration, the the search step is either increased or decreased to adapt
+the progression speed. A composite step can occasionally be done. \cr
+The calibration algorithm stops when the search step becomes smaller than a predefined threshold. \cr
+}
+\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_Michel)
+
+## calibration
+OutputsCalib <- Calibration_Michel(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, Claude Michel (August 2013)
+}
+\references{
+Michel, C. (1991),
+ Hydrologie appliquée aux petits bassins ruraux, Hydrology handbook (in French), Cemagref, Antony, France.
+}
+\seealso{
+\code{\link{Calibration}}, \code{\link{Calibration_optim}},
+ \code{\link{RunModel_GR4J}}, \code{\link{TransfoParam_GR4J}}, \code{\link{ErrorCrit_RMSE}},
+ \code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}},
+ \code{\link{CreateInputsCrit}}, \code{\link{CreateCalibOptions}}.
+}
+
diff --git a/man/DataAltiExtrapolation_HBAN.Rd b/man/DataAltiExtrapolation_Valery.Rd
similarity index 91%
rename from man/DataAltiExtrapolation_HBAN.Rd
rename to man/DataAltiExtrapolation_Valery.Rd
index 1d71705c..6a95b62a 100644
--- a/man/DataAltiExtrapolation_HBAN.Rd
+++ b/man/DataAltiExtrapolation_Valery.Rd
@@ -1,11 +1,11 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DataAltiExtrapolation_HBAN.R
+% Please edit documentation in R/DataAltiExtrapolation_Valery.R
\encoding{UTF-8}
-\name{DataAltiExtrapolation_HBAN}
-\alias{DataAltiExtrapolation_HBAN}
-\title{Altitudinal extrapolation of precipitation and temperature series}
+\name{DataAltiExtrapolation_Valery}
+\alias{DataAltiExtrapolation_Valery}
+\title{Altitudinal extrapolation of precipitation and temperature series described by A. Valéry}
\usage{
-DataAltiExtrapolation_HBAN(DatesR, Precip, TempMean, TempMin = NULL,
+DataAltiExtrapolation_Valery(DatesR, Precip, TempMean, TempMin = NULL,
TempMax = NULL, ZInputs, HypsoData, NLayers, quiet = FALSE)
}
\arguments{
@@ -49,7 +49,7 @@ Forcing data (precipitation and air temperature) are extrapolated using gradient
This function is used by the \emph{CreateInputsModel} function. \cr
}
\author{
-Laurent Coron, Pierre Brigode (June 2014)
+Laurent Coron, Audrey Valéry, Pierre Brigode (June 2014)
}
\references{
Turcotte, R., L.-G. Fortin, V. Fortin, J.-P. Fortin and J.-P. Villeneuve (2007),
diff --git a/tests/example_Calibration_HBAN.R b/tests/example_Calibration_Michel.R
similarity index 95%
rename from tests/example_Calibration_HBAN.R
rename to tests/example_Calibration_Michel.R
index 75b7832f..efc26721 100644
--- a/tests/example_Calibration_HBAN.R
+++ b/tests/example_Calibration_Michel.R
@@ -18,10 +18,10 @@ 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_HBAN)
+CalibOptions <- CreateCalibOptions(FUN_MOD=RunModel_GR4J,FUN_CALIB=Calibration_Michel)
## calibration
-OutputsCalib <- Calibration_HBAN(InputsModel=InputsModel,RunOptions=RunOptions,
+OutputsCalib <- Calibration_Michel(InputsModel=InputsModel,RunOptions=RunOptions,
InputsCrit=InputsCrit,CalibOptions=CalibOptions,
FUN_MOD=RunModel_GR4J,FUN_CRIT=ErrorCrit_NSE)
--
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