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Commit 9affb66e authored by Delaigue Olivier's avatar Delaigue Olivier
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v1.6.9.32 man: review style in many help pages

parent 4390ce3e
dev 115-add-pcict-date-format-managment 118-plot-outputsmodel-remove-case-sensitivity-to-the-which-argument 136-decreased-performance-of-calibration-execution-time 161-runmodel_lag-proposal-for-a-better-transformation-and-screening-of-the-parameters 165-add-missing-isintstore-argument-in-createcaliboptions 171-check-error-direct-call-of-as-data-frame-posixct-is-deprecated-use-as-data-frame-vector-or-as 191-speed-up-runmodel_lag-when-it-is-used-alone 33-merge-airgr-and-airgrplus-functions 96-parallelize-the-grid-screening-step-during-calibration master rmOptions CRAN_v1.7.6 CRAN_v1.7.5 CRAN_v1.7.4 CRAN_v1.7.3 CRAN_v1.7.2 CRAN_v1.7.1 CRAN_v1.7.0 CRAN_v1.6.12 CRAN_v1.6.11 CRAN_v1.6.10.4
1 merge request!29CRAN v1.6.10.4
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DESCRIPTION
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Package: airGR Package: airGR
Type: Package Type: Package
Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling
Version: 1.6.9.31 Version: 1.6.9.32
Date: 2021-01-25 Date: 2021-01-26
Authors@R: c( Authors@R: c(
person("Laurent", "Coron", role = c("aut", "trl"), comment = c(ORCID = "0000-0002-1503-6204")), person("Laurent", "Coron", role = c("aut", "trl"), comment = c(ORCID = "0000-0002-1503-6204")),
person("Olivier", "Delaigue", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7668-8468"), email = "airGR@inrae.fr"), person("Olivier", "Delaigue", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7668-8468"), email = "airGR@inrae.fr"),
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man/CreateCalibOptions.Rd
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...@@ -80,7 +80,7 @@ CreateCalibOptions(FUN_MOD, FUN_CALIB = Calibration_Michel, ...@@ -80,7 +80,7 @@ CreateCalibOptions(FUN_MOD, FUN_CALIB = Calibration_Michel,
Users wanting to use \code{FUN_MOD}, \code{FUN_CALIB} or \code{FUN_TRANSFO} functions that are not included in Users wanting to use \code{FUN_MOD}, \code{FUN_CALIB} or \code{FUN_TRANSFO} functions that are not included in
the package must create their own \code{CalibOptions} object accordingly. \cr the package must create their own \code{CalibOptions} object accordingly. \cr
## ---- CemaNeige version ## --- CemaNeige version
If \code{IsHyst = FALSE}, the original CemaNeige version from Valéry et al. (2014) is used. \cr If \code{IsHyst = FALSE}, the original CemaNeige version from Valéry et al. (2014) is used. \cr
If \code{IsHyst = TRUE}, the CemaNeige version from Riboust et al. (2019) is used. Compared to the original version, this version of CemaNeige needs two more parameters and it includes a representation of the hysteretic relationship between the Snow Cover Area (SCA) and the Snow Water Equivalent (SWE) in the catchment. The hysteresis included in airGR is the Modified Linear hysteresis (LH*); it is represented on panel b) of Fig. 3 in Riboust et al. (2019). Riboust et al. (2019) advise to use the LH* version of CemaNeige with parameters calibrated using an objective function combining 75 \% of KGE calculated on discharge simulated from a rainfall-runoff model compared to observed discharge and 5 \% of KGE calculated on SCA on 5 CemaNeige elevation bands compared to satellite (e.g. MODIS) SCA (see Eq. (18), Table 3 and Fig. 6). Riboust et al. (2019)'s tests were realized with GR4J as the chosen rainfall-runoff model. \cr If \code{IsHyst = TRUE}, the CemaNeige version from Riboust et al. (2019) is used. Compared to the original version, this version of CemaNeige needs two more parameters and it includes a representation of the hysteretic relationship between the Snow Cover Area (SCA) and the Snow Water Equivalent (SWE) in the catchment. The hysteresis included in airGR is the Modified Linear hysteresis (LH*); it is represented on panel b) of Fig. 3 in Riboust et al. (2019). Riboust et al. (2019) advise to use the LH* version of CemaNeige with parameters calibrated using an objective function combining 75 \% of KGE calculated on discharge simulated from a rainfall-runoff model compared to observed discharge and 5 \% of KGE calculated on SCA on 5 CemaNeige elevation bands compared to satellite (e.g. MODIS) SCA (see Eq. (18), Table 3 and Fig. 6). Riboust et al. (2019)'s tests were realized with GR4J as the chosen rainfall-runoff model. \cr
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man/CreateInputsCrit.Rd
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...@@ -73,11 +73,11 @@ To calculate composite or multiple criteria, it is necessary to use the \code{Er ...@@ -73,11 +73,11 @@ To calculate composite or multiple criteria, it is necessary to use the \code{Er
\details{ \details{
Users wanting to use \code{FUN_CRIT} functions that are not included in the package must create their own InputsCrit object accordingly. \cr \cr Users wanting to use \code{FUN_CRIT} functions that are not included in the package must create their own InputsCrit object accordingly. \cr \cr
## ---- Period of calculation ## --- Period of calculation
Criteria can be calculated over discontinuous periods (i.e. only over winter periods, or when observed discharge is below a certain threshold). To do so, please indicate in \code{Bool_Crit} which indices must be used for calcullation. Discontinuous periods are allowed in the \code{Bool_Crit} argument. Criteria can be calculated over discontinuous periods (i.e. only over winter periods, or when observed discharge is below a certain threshold). To do so, please indicate in \code{Bool_Crit} which indices must be used for calcullation. Discontinuous periods are allowed in the \code{Bool_Crit} argument.
## ---- Transformations ## --- Transformations
Transformations are simple functions applied to the observed and simulated variables used in order to change their distribution. Transformations are often used in hydrology for modifying the weight put on errors made for high flows or low flows. The following transformations are available: \cr \cr Transformations are simple functions applied to the observed and simulated variables used in order to change their distribution. Transformations are often used in hydrology for modifying the weight put on errors made for high flows or low flows. The following transformations are available: \cr \cr
\itemize{ \itemize{
...@@ -93,11 +93,11 @@ We do not advise computing KGE or KGE' with log-transformation as it might be wr ...@@ -93,11 +93,11 @@ We do not advise computing KGE or KGE' with log-transformation as it might be wr
In order to make sure that KGE and KGE2 remain dimensionless and are not impacted by zero values, the Box-Cox transformation (\code{transfo = "boxcox"}) uses the formulation given in Equation 10 of Santos et al. (2018). Lambda is set to 0.25 accordingly. \cr \cr In order to make sure that KGE and KGE2 remain dimensionless and are not impacted by zero values, the Box-Cox transformation (\code{transfo = "boxcox"}) uses the formulation given in Equation 10 of Santos et al. (2018). Lambda is set to 0.25 accordingly. \cr \cr
The syntax of the power transformation allows a numeric or a string of characters. For example for a squared transformation, the following can be used: \code{transfo = 2}, \code{transfo = "2"} or \code{transfo = "^2"}. Negative values are allowed. Fraction values are not allowed (e.g., \code{"-1/2"} must instead be written \code{"-0.5"}).\cr \cr The syntax of the power transformation allows a numeric or a string of characters. For example for a squared transformation, the following can be used: \code{transfo = 2}, \code{transfo = "2"} or \code{transfo = "^2"}. Negative values are allowed. Fraction values are not allowed (e.g., \code{"-1/2"} must instead be written \code{"-0.5"}).\cr \cr
## ---- The epsilon value ## --- The epsilon value
The epsilon value is useful when \code{"log"} or \code{"inv"} transformations are used (to avoid calculation of the inverse or of the logarithm of zero). If an epsilon value is provided, then it is added to the observed and simulated variable time series at each time step and before the application of a transformation. The epsilon value has no effect when the \code{"boxcox"} transformation is used. The impact of this value and a recommendation about the epsilon value to use (usually one hundredth of average observation) are discussed in Pushpalatha et al. (2012) for NSE and in Santos et al. (2018) for KGE and KGE'. \cr \cr The epsilon value is useful when \code{"log"} or \code{"inv"} transformations are used (to avoid calculation of the inverse or of the logarithm of zero). If an epsilon value is provided, then it is added to the observed and simulated variable time series at each time step and before the application of a transformation. The epsilon value has no effect when the \code{"boxcox"} transformation is used. The impact of this value and a recommendation about the epsilon value to use (usually one hundredth of average observation) are discussed in Pushpalatha et al. (2012) for NSE and in Santos et al. (2018) for KGE and KGE'. \cr \cr
## ---- Single, multiple or composite criteria calculation ## --- Single, multiple or composite criteria calculation
Users can set the following arguments as atomic or list: \code{FUN_CRIT}, \code{Obs}, \code{VarObs}, \code{BoolCrit}, \code{transfo}, \code{Weights}. If the list format is chosen, all the lists must have the same length. \cr Users can set the following arguments as atomic or list: \code{FUN_CRIT}, \code{Obs}, \code{VarObs}, \code{BoolCrit}, \code{transfo}, \code{Weights}. If the list format is chosen, all the lists must have the same length. \cr
Calculation of a single criterion (e.g. NSE computed on discharge) is prepared by providing to \code{CreateInputsCrit} arguments atomics only. \cr Calculation of a single criterion (e.g. NSE computed on discharge) is prepared by providing to \code{CreateInputsCrit} arguments atomics only. \cr
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man/CreateRunOptions.Rd
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...@@ -72,11 +72,11 @@ CreateRunOptions(FUN_MOD, InputsModel, ...@@ -72,11 +72,11 @@ CreateRunOptions(FUN_MOD, InputsModel,
Users wanting to use \code{FUN_MOD} functions that are not included in Users wanting to use \code{FUN_MOD} functions that are not included in
the package must create their own \code{RunOptions} object accordingly. the package must create their own \code{RunOptions} object accordingly.
## ---- IndPeriod_WarmUp and IndPeriod_Run ## --- IndPeriod_WarmUp and IndPeriod_Run
Since the hydrological models included in airGR are continuous models, meaning that internal states of the models are propagated to the next time step, \code{IndPeriod_WarmUp} and \code{IndPeriod_Run} must be continuous periods, represented by continuous indices values; no gaps are allowed. To calculate criteria or to calibrate a model over discontinuous periods, please see the \code{Bool_Crit} argument of the \code{\link{CreateInputsCrit}} function. Since the hydrological models included in airGR are continuous models, meaning that internal states of the models are propagated to the next time step, \code{IndPeriod_WarmUp} and \code{IndPeriod_Run} must be continuous periods, represented by continuous indices values; no gaps are allowed. To calculate criteria or to calibrate a model over discontinuous periods, please see the \code{Bool_Crit} argument of the \code{\link{CreateInputsCrit}} function.
## ---- Initialisation options ## --- Initialisation options
The model initialisation options can either be set to a default configuration or be defined by the user. The model initialisation options can either be set to a default configuration or be defined by the user.
...@@ -111,7 +111,7 @@ However, it is also possible to perform a long-term initialisation if other indi ...@@ -111,7 +111,7 @@ However, it is also possible to perform a long-term initialisation if other indi
} }
} }
## ---- CemaNeige version ## --- CemaNeige version
If \code{IsHyst = FALSE}, the original CemaNeige version from Valéry et al. (2014) is used. \cr If \code{IsHyst = FALSE}, the original CemaNeige version from Valéry et al. (2014) is used. \cr
If \code{IsHyst = TRUE}, the CemaNeige version from Riboust et al. (2019) is used. Compared to the original version, this version of CemaNeige needs two more parameters and it includes a representation of the hysteretic relationship between the Snow Cover Area (SCA) and the Snow Water Equivalent (SWE) in the catchment. The hysteresis included in airGR is the Modified Linear hysteresis (LH*); it is represented on panel b) of Fig. 3 in Riboust et al. (2019). Riboust et al. (2019) advise to use the LH* version of CemaNeige with parameters calibrated using an objective function combining 75 \% of KGE calculated on discharge simulated from a rainfall-runoff model compared to observed discharge and 5 \% of KGE calculated on SCA on 5 CemaNeige elevation bands compared to satellite (e.g. MODIS) SCA (see Eq. (18), Table 3 and Fig. 6). Riboust et al. (2019)'s tests were realized with GR4J as the chosen rainfall-runoff model. \cr If \code{IsHyst = TRUE}, the CemaNeige version from Riboust et al. (2019) is used. Compared to the original version, this version of CemaNeige needs two more parameters and it includes a representation of the hysteretic relationship between the Snow Cover Area (SCA) and the Snow Water Equivalent (SWE) in the catchment. The hysteresis included in airGR is the Modified Linear hysteresis (LH*); it is represented on panel b) of Fig. 3 in Riboust et al. (2019). Riboust et al. (2019) advise to use the LH* version of CemaNeige with parameters calibrated using an objective function combining 75 \% of KGE calculated on discharge simulated from a rainfall-runoff model compared to observed discharge and 5 \% of KGE calculated on SCA on 5 CemaNeige elevation bands compared to satellite (e.g. MODIS) SCA (see Eq. (18), Table 3 and Fig. 6). Riboust et al. (2019)'s tests were realized with GR4J as the chosen rainfall-runoff model. \cr
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man/Param_Sets_GR4J.Rd
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...@@ -56,7 +56,7 @@ Param_Sets_GR4J <- as.matrix(Param_Sets_GR4J) ...@@ -56,7 +56,7 @@ Param_Sets_GR4J <- as.matrix(Param_Sets_GR4J)
InputsModel <- CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR, InputsModel <- CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR,
Precip = BasinObs$P, PotEvap = BasinObs$E) Precip = BasinObs$P, PotEvap = BasinObs$E)
## ---- calibration step ## --- calibration step
## short calibration period selection (< 6 months) ## short calibration period selection (< 6 months)
Ind_Cal <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"), Ind_Cal <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
...@@ -82,7 +82,7 @@ OutputsCrit_Loop <- apply(Param_Sets_GR4J, 1, function(Param) { ...@@ -82,7 +82,7 @@ OutputsCrit_Loop <- apply(Param_Sets_GR4J, 1, function(Param) {
Param_Best <- unlist(Param_Sets_GR4J[which.max(OutputsCrit_Loop), ]) Param_Best <- unlist(Param_Sets_GR4J[which.max(OutputsCrit_Loop), ])
## ---- validation step ## --- validation step
## validation period selection ## validation period selection
Ind_Val <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-03-01"), Ind_Val <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-03-01"),
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man/RunModel_CemaNeige.Rd
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...@@ -79,7 +79,7 @@ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-0 ...@@ -79,7 +79,7 @@ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-0
which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31")) which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
## ---- original version of CemaNeige ## --- original version of CemaNeige
## preparation of the RunOptions object ## preparation of the RunOptions object
RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeige, InputsModel = InputsModel, RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeige, InputsModel = InputsModel,
...@@ -94,7 +94,7 @@ OutputsModel <- RunModel_CemaNeige(InputsModel = InputsModel, ...@@ -94,7 +94,7 @@ OutputsModel <- RunModel_CemaNeige(InputsModel = InputsModel,
plot(OutputsModel) plot(OutputsModel)
## ---- version of CemaNeige with the Linear Hysteresis ## --- version of CemaNeige with the Linear Hysteresis
## preparation of the RunOptions object ## preparation of the RunOptions object
RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeige, InputsModel = InputsModel, RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeige, InputsModel = InputsModel,
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man/RunModel_CemaNeigeGR4H.Rd
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...@@ -108,7 +108,7 @@ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d \%H:\%M")=="2 ...@@ -108,7 +108,7 @@ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d \%H:\%M")=="2
which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d \%H:\%M")=="2008-12-31 23:00")) which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d \%H:\%M")=="2008-12-31 23:00"))
## ---- original version of CemaNeige ## --- original version of CemaNeige
## preparation of the RunOptions object ## preparation of the RunOptions object
RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeigeGR4H, InputsModel = InputsModel, RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeigeGR4H, InputsModel = InputsModel,
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man/RunModel_CemaNeigeGR4J.Rd
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...@@ -104,7 +104,7 @@ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-0 ...@@ -104,7 +104,7 @@ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-0
which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31")) which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
## ---- original version of CemaNeige ## --- original version of CemaNeige
## preparation of the RunOptions object ## preparation of the RunOptions object
RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeigeGR4J, InputsModel = InputsModel, RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeigeGR4J, InputsModel = InputsModel,
...@@ -125,7 +125,7 @@ InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsMo ...@@ -125,7 +125,7 @@ InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsMo
OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel) OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
## ---- version of CemaNeige with the Linear Hysteresis ## --- version of CemaNeige with the Linear Hysteresis
## preparation of the RunOptions object ## preparation of the RunOptions object
RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeigeGR4J, InputsModel = InputsModel, RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeigeGR4J, InputsModel = InputsModel,
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man/RunModel_CemaNeigeGR5H.Rd
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...@@ -109,7 +109,7 @@ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d \%H:\%M")=="2 ...@@ -109,7 +109,7 @@ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d \%H:\%M")=="2
which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d \%H:\%M")=="2008-12-31 23:00")) which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d \%H:\%M")=="2008-12-31 23:00"))
## ---- original version of CemaNeige ## --- original version of CemaNeige
## Imax computation ## Imax computation
Imax <- Imax(InputsModel = InputsModel, IndPeriod_Run = Ind_Run, Imax <- Imax(InputsModel = InputsModel, IndPeriod_Run = Ind_Run,
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man/RunModel_CemaNeigeGR6J.Rd
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...@@ -108,7 +108,7 @@ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-0 ...@@ -108,7 +108,7 @@ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-0
which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31")) which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
## ---- original version of CemaNeige ## --- original version of CemaNeige
## preparation of the RunOptions object ## preparation of the RunOptions object
RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeigeGR6J, InputsModel = InputsModel, RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeigeGR6J, InputsModel = InputsModel,
...@@ -129,7 +129,7 @@ InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsMo ...@@ -129,7 +129,7 @@ InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsMo
OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel) OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
## ---- version of CemaNeige with the Linear Hysteresis ## --- version of CemaNeige with the Linear Hysteresis
## preparation of the RunOptions object ## preparation of the RunOptions object
RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeigeGR6J, InputsModel = InputsModel, RunOptions <- CreateRunOptions(FUN_MOD = RunModel_CemaNeigeGR6J, InputsModel = InputsModel,
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man/TransfoParam.Rd
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...@@ -55,7 +55,7 @@ TransfoParam_CemaNeigeHyst(ParamIn, Direction) ...@@ -55,7 +55,7 @@ TransfoParam_CemaNeigeHyst(ParamIn, Direction)
\examples{ \examples{
library(airGR) library(airGR)
## ---- generic function ## --- generic function
## transformation Raw -> Transformed for the GR4J model ## transformation Raw -> Transformed for the GR4J model
Xraw <- matrix(c(+221.41, -3.63, +30.00, +1.37, Xraw <- matrix(c(+221.41, -3.63, +30.00, +1.37,
...@@ -72,7 +72,7 @@ Xtran <- matrix(c(+3.60, -2.00, +3.40, -9.10, ...@@ -72,7 +72,7 @@ Xtran <- matrix(c(+3.60, -2.00, +3.40, -9.10,
Xraw <- TransfoParam(ParamIn = Xtran, Direction = "TR", FUN_TRANSFO = TransfoParam_GR4J) Xraw <- TransfoParam(ParamIn = Xtran, Direction = "TR", FUN_TRANSFO = TransfoParam_GR4J)
## ---- specific function ## --- specific function
## transformation Raw -> Transformed for the GR4J model ## transformation Raw -> Transformed for the GR4J model
Xraw <- matrix(c(+221.41, -3.63, +30.00, +1.37, Xraw <- matrix(c(+221.41, -3.63, +30.00, +1.37,
......
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