Commit 3f8d9e53 authored by Delaigue Olivier's avatar Delaigue Olivier
Browse files

v1.2.9.29 CLEAN: add varObs = "Q" argument of CreateInputsCrit in Calibration...

v1.2.9.29 CLEAN: add varObs = "Q" argument of CreateInputsCrit in Calibration and Create* docs and deprectad FUN_CALIB and FUN_CRIT args in Create* docs
parent a5a4cd12
Package: airGR
Type: Package
Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling
Version: 1.2.9.28
Version: 1.2.9.29
Date: 2019-03-20
Authors@R: c(
person("Laurent", "Coron", role = c("aut", "trl"), comment = c(ORCID = "0000-0002-1503-6204")),
......
......@@ -13,7 +13,7 @@ output:
### 1.2.9.28 Release Notes (2019-03-20)
### 1.2.9.29 Release Notes (2019-03-20)
......
......@@ -27,7 +27,7 @@ Calibration(InputsModel, RunOptions, InputsCrit, CalibOptions, FUN_MOD,
\item{FUN_CRIT}{[function] error criterion function (e.g. \code{\link{ErrorCrit_RMSE}}, \code{\link{ErrorCrit_NSE}})}
\item{FUN_CALIB}{(optional) [function] calibration algorithm function (e.g. \code{\link{Calibration_Michel}}), \code{default = Calibration_Michel}}
\item{FUN_CALIB}{(deprecated) [function] calibration algorithm function (e.g. \code{\link{Calibration_Michel}}), \code{default = Calibration_Michel}}
\item{FUN_TRANSFO}{(optional) [function] model parameters transformation function, if the \code{FUN_MOD} used is native in the package \code{FUN_TRANSFO} is automatically defined}
......@@ -65,7 +65,7 @@ RunOptions <- CreateRunOptions(FUN_MOD = RunModel_GR4J,
## calibration criterion: preparation of the InputsCrit object
InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel,
RunOptions = RunOptions, Qobs = BasinObs$Qmm[Ind_Run])
RunOptions = RunOptions, obs = BasinObs$Qmm[Ind_Run], varObs = "Q")
## preparation of CalibOptions object
CalibOptions <- CreateCalibOptions(FUN_MOD = RunModel_GR4J, FUN_CALIB = Calibration_Michel)
......@@ -73,7 +73,7 @@ CalibOptions <- CreateCalibOptions(FUN_MOD = RunModel_GR4J, FUN_CALIB = Calibrat
## calibration
OutputsCalib <- Calibration(InputsModel = InputsModel, RunOptions = RunOptions,
InputsCrit = InputsCrit, CalibOptions = CalibOptions,
FUN_MOD = RunModel_GR4J, FUN_CRIT = ErrorCrit_NSE,
FUN_MOD = RunModel_GR4J,
FUN_CALIB = Calibration_Michel)
## simulation
......@@ -86,12 +86,12 @@ plot(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])
RunOptions = RunOptions, obs = BasinObs$Qmm[Ind_Run], varObs = "Q")
OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
## efficiency criterion: Kling-Gupta Efficiency
InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_KGE, InputsModel = InputsModel,
RunOptions = RunOptions, Qobs = BasinObs$Qmm[Ind_Run])
RunOptions = RunOptions, obs = BasinObs$Qmm[Ind_Run], varObs = "Q")
OutputsCrit <- ErrorCrit_KGE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
}
......
......@@ -25,7 +25,7 @@ Calibration_Michel(InputsModel, RunOptions, InputsCrit, CalibOptions,
\item{FUN_MOD}{[function] hydrological model function (e.g. \code{\link{RunModel_GR4J}}, \code{\link{RunModel_CemaNeigeGR4J}})}
\item{FUN_CRIT}{[function] error criterion function (e.g. \code{\link{ErrorCrit_RMSE}}, \code{\link{ErrorCrit_NSE}})}
\item{FUN_CRIT}{(deprecated) [function] error criterion function (e.g. \code{\link{ErrorCrit_RMSE}}, \code{\link{ErrorCrit_NSE}})}
\item{FUN_TRANSFO}{(optional) [function] model parameters transformation function, if the \code{FUN_MOD} used is native in the package \code{FUN_TRANSFO} is automatically defined}
......@@ -35,17 +35,17 @@ Calibration_Michel(InputsModel, RunOptions, InputsCrit, CalibOptions,
\value{
[list] list containing the function outputs organised as follows:
\tabular{ll}{
\emph{$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
}
\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{$CritBestValue} \tab [numeric] theoretical best criterion value \cr
}
}
......@@ -96,7 +96,7 @@ RunOptions <- CreateRunOptions(FUN_MOD = RunModel_GR4J, InputsModel = InputsMode
## calibration criterion: preparation of the InputsCrit object
InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel,
RunOptions = RunOptions, Qobs = BasinObs$Qmm[Ind_Run])
RunOptions = RunOptions, obs = BasinObs$Qmm[Ind_Run], varObs = "Q")
## preparation of CalibOptions object
CalibOptions <- CreateCalibOptions(FUN_MOD = RunModel_GR4J, FUN_CALIB = Calibration_Michel)
......@@ -104,7 +104,7 @@ CalibOptions <- CreateCalibOptions(FUN_MOD = RunModel_GR4J, FUN_CALIB = Calibrat
## calibration
OutputsCalib <- Calibration_Michel(InputsModel = InputsModel, RunOptions = RunOptions,
InputsCrit = InputsCrit, CalibOptions = CalibOptions,
FUN_MOD = RunModel_GR4J, FUN_CRIT = ErrorCrit_NSE)
FUN_MOD = RunModel_GR4J)
## simulation
Param <- OutputsCalib$ParamFinalR
......@@ -116,12 +116,12 @@ plot(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])
RunOptions = RunOptions, obs = BasinObs$Qmm[Ind_Run], varObs = "Q")
OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
## efficiency criterion: Kling-Gupta Efficiency
InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_KGE, InputsModel = InputsModel,
RunOptions = RunOptions, Qobs = BasinObs$Qmm[Ind_Run])
RunOptions = RunOptions, obs = BasinObs$Qmm[Ind_Run], varObs = "Q")
OutputsCrit <- ErrorCrit_KGE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
}
......
......@@ -58,12 +58,12 @@ CreateCalibOptions(FUN_MOD, FUN_CALIB = Calibration_Michel,
}
\value{
[list] object of class \emph{CalibOptions} containing the data required to evaluate the model outputs; it can include the following:
\tabular{ll}{
\emph{$FixedParam } \tab [numeric] vector giving the values to allocate to non-optimised parameter values \cr
\emph{$SearchRanges } \tab [numeric] matrix giving the ranges of raw parameters \cr
\emph{$StartParamList } \tab [numeric] matrix of parameter sets used for grid-screening calibration procedure \cr
\emph{$StartParamDistrib} \tab [numeric] matrix of parameter values used for grid-screening calibration procedure \cr
}
\tabular{ll}{
\emph{$FixedParam } \tab [numeric] vector giving the values to allocate to non-optimised parameter values \cr
\emph{$SearchRanges } \tab [numeric] matrix giving the ranges of raw parameters \cr
\emph{$StartParamList } \tab [numeric] matrix of parameter sets used for grid-screening calibration procedure \cr
\emph{$StartParamDistrib} \tab [numeric] matrix of parameter values used for grid-screening calibration procedure \cr
}
}
......@@ -98,7 +98,7 @@ RunOptions <- CreateRunOptions(FUN_MOD = RunModel_GR4J,
## calibration criterion: preparation of the InputsCrit object
InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel,
RunOptions = RunOptions, Qobs = BasinObs$Qmm[Ind_Run])
RunOptions = RunOptions, obs = BasinObs$Qmm[Ind_Run], varObs = "Q")
## preparation of CalibOptions object
CalibOptions <- CreateCalibOptions(FUN_MOD = RunModel_GR4J, FUN_CALIB = Calibration_Michel)
......@@ -106,7 +106,7 @@ CalibOptions <- CreateCalibOptions(FUN_MOD = RunModel_GR4J, FUN_CALIB = Calibrat
## calibration
OutputsCalib <- Calibration(InputsModel = InputsModel, RunOptions = RunOptions,
InputsCrit = InputsCrit, CalibOptions = CalibOptions,
FUN_MOD = RunModel_GR4J, FUN_CRIT = ErrorCrit_NSE,
FUN_MOD = RunModel_GR4J,
FUN_CALIB = Calibration_Michel)
## simulation
......@@ -119,12 +119,12 @@ plot(OutputsModel, Qobs = BasinObs$Qmm[Ind_Run])
## efficiency criterion: Nash-Sutcliffe Efficiency
InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel,
RunOptions = RunOptions, Qobs = BasinObs$Qmm[Ind_Run])
RunOptions = RunOptions, obs = BasinObs$Qmm[Ind_Run], varObs = "Q")
OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
## efficiency criterion: Kling-Gupta Efficiency
InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_KGE, InputsModel = InputsModel,
RunOptions = RunOptions, Qobs = BasinObs$Qmm[Ind_Run])
RunOptions = RunOptions, obs = BasinObs$Qmm[Ind_Run], varObs = "Q")
OutputsCrit <- ErrorCrit_KGE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
}
......
......@@ -44,13 +44,13 @@ CreateInputsModel(FUN_MOD, DatesR, Precip, PrecipScale = TRUE, PotEvap = NULL,
\value{
[list] object of class \emph{InputsModel} containing the data required to evaluate the model outputs; it can include the following:
\tabular{ll}{
\emph{$DatesR } \tab [POSIXlt] vector of dates \cr
\emph{$Precip } \tab [numeric] time series of total precipitation (catchment average) [mm/time step] \cr
\emph{$PotEvap } \tab [numeric] time series of potential evapotranspiration (catchment average) [mm/time step], \cr\tab defined if FUN_MOD includes GR4H, GR4J, GR5J, GR6J, GR2M or GR1A \cr \cr
\emph{$LayerPrecip } \tab [list] list of time series of precipitation (layer average) [mm/time step], \cr\tab defined if \code{FUN_MOD} includes CemaNeige \cr \cr
\emph{$LayerTempMean } \tab [list] list of time series of mean air temperature (layer average) [°C], \cr\tab defined if \code{FUN_MOD} includes CemaNeige \cr \cr
\emph{$LayerFracSolidPrecip} \tab [list] list of time series of solid precipitation fraction (layer average) [-], \cr\tab defined if \code{FUN_MOD} includes CemaNeige \cr \cr
\tabular{ll}{
\emph{$DatesR } \tab [POSIXlt] vector of dates \cr
\emph{$Precip } \tab [numeric] time series of total precipitation (catchment average) [mm/time step] \cr
\emph{$PotEvap } \tab [numeric] time series of potential evapotranspiration (catchment average) [mm/time step], \cr\tab defined if FUN_MOD includes GR4H, GR4J, GR5J, GR6J, GR2M or GR1A \cr \cr
\emph{$LayerPrecip } \tab [list] list of time series of precipitation (layer average) [mm/time step], \cr\tab defined if \code{FUN_MOD} includes CemaNeige \cr \cr
\emph{$LayerTempMean } \tab [list] list of time series of mean air temperature (layer average) [°C], \cr\tab defined if \code{FUN_MOD} includes CemaNeige \cr \cr
\emph{$LayerFracSolidPrecip} \tab [list] list of time series of solid precipitation fraction (layer average) [-], \cr\tab defined if \code{FUN_MOD} includes CemaNeige \cr \cr
}
}
......@@ -95,7 +95,7 @@ plot(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])
RunOptions = RunOptions, obs = BasinObs$Qmm[Ind_Run], varObs = "Q")
OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
}
......
......@@ -49,15 +49,15 @@ CreateRunOptions(FUN_MOD, InputsModel,
\value{
[list] object of class \emph{RunOptions} containing the data required to evaluate the model outputs; it can include the following:
\tabular{ll}{
\emph{IndPeriod_WarmUp } \tab [numeric] index of period to be used for the model warm-up [-] \cr
\emph{IndPeriod_Run } \tab [numeric] index of period to be used for the model run [-] \cr
\emph{IniStates } \tab [numeric] vector of initial model states [mm and °C] \cr
\emph{IniResLevels } \tab [numeric] vector of initial filling rates for production and routing stores [-] and level for the exponential store for GR6J [mm]\cr
\emph{Outputs_Cal } \tab [character] character vector giving only the outputs needed for the calibration \cr
\emph{Outputs_Sim } \tab [character] character vector giving the requested outputs \cr
\emph{MeanAnSolidPrecip} \tab [numeric] vector giving the annual mean of average solid precipitation for each layer [mm/y] \cr
}
\tabular{ll}{
\emph{IndPeriod_WarmUp } \tab [numeric] index of period to be used for the model warm-up [-] \cr
\emph{IndPeriod_Run } \tab [numeric] index of period to be used for the model run [-] \cr
\emph{IniStates } \tab [numeric] vector of initial model states [mm and °C] \cr
\emph{IniResLevels } \tab [numeric] vector of initial filling rates for production and routing stores [-] and level for the exponential store for GR6J [mm]\cr
\emph{Outputs_Cal } \tab [character] character vector giving only the outputs needed for the calibration \cr
\emph{Outputs_Sim } \tab [character] character vector giving the requested outputs \cr
\emph{MeanAnSolidPrecip} \tab [numeric] vector giving the annual mean of average solid precipitation for each layer [mm/y] \cr
}
}
......@@ -135,7 +135,7 @@ plot(OutputsModel, Qobs = BasinObs$Qmm[Ind_Run])
## efficiency criterion: Nash-Sutcliffe Efficiency
InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel,
RunOptions = RunOptions, Qobs = BasinObs$Qmm[Ind_Run])
RunOptions = RunOptions, obs = BasinObs$Qmm[Ind_Run], varObs = "Q")
OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
}
......
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