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

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
3f8d9e53 · Delaigue Olivier · a5a4cd12 · 3f8d9e53 · 3f8d9e53 · 3f8d9e53
Commit 3f8d9e53 authored 6 years ago by Delaigue Olivier
Hide whitespace changes
Inline Side-by-side

Showing

with 51 additions and 51 deletions
+51 -51
--- a/DESCRIPTION
+++ b/DESCRIPTION
 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")),

--- a/NEWS.rmd
+++ b/NEWS.rmd
@@ -13,7 +13,7 @@ output:



-### 1.2.9.28 Release Notes (2019-03-20) 
+### 1.2.9.29 Release Notes (2019-03-20) 




--- a/man/Calibration.Rd
+++ b/man/Calibration.Rd
@@ -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)
 }


--- a/man/Calibration_Michel.Rd
+++ b/man/Calibration_Michel.Rd
@@ -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)
 }


--- a/man/CreateCalibOptions.Rd
+++ b/man/CreateCalibOptions.Rd
@@ -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)

 }

--- a/man/CreateInputsModel.Rd
+++ b/man/CreateInputsModel.Rd
@@ -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)

 }

--- a/man/CreateRunOptions.Rd
+++ b/man/CreateRunOptions.Rd
@@ -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)
 }