From d5943d287ae04df4e827b379e81b3cc1fa39808c Mon Sep 17 00:00:00 2001
From: Dorchies David <david.dorchies@inrae.fr>
Date: Sun, 12 Dec 2021 14:02:46 +0100
Subject: [PATCH] feat: seemless integration of airGR into airGRiwrm
- import airGR with "Depends"
- remove all library(airGR) and airGR::FUN
Closes #63
---
.Rbuildignore | 1 +
DESCRIPTION | 6 +-
NAMESPACE | 4 +
R/Calibration.GRiwrmInputsModel.R | 1 +
R/Calibration.InputsModel.R | 6 +-
R/CreateCalibOptions.GRiwrmInputsModel.R | 8 +-
R/CreateCalibOptions.InputsModel.R | 10 ---
R/CreateCalibOptions.R | 43 +++++++++-
R/CreateGRiwrm.R | 23 +----
R/CreateInputsCrit.GRiwrmInputsModel.R | 3 +-
R/CreateInputsModel.GRiwrm.R | 42 +---------
R/CreateInputsModel.R | 10 +++
R/CreateInputsModel.default.R | 12 ---
R/CreateRunOptions.GRiwrmInputsModel.R | 6 +-
R/CreateRunOptions.InputsModel.R | 8 --
R/CreateRunOptions.R | 35 +++++++-
R/CreateSupervisor.R | 1 -
R/RunModel.GR.R | 4 +-
R/RunModel.GRiwrmInputsModel.R | 65 ++++++++++-----
man-roxygen/param_x.R | 2 +
man/CreateCalibOptions.Rd | 18 ++--
man/CreateGRiwrm.Rd | 73 ++++++++++++++--
man/CreateInputsCrit.Rd | 2 +-
man/CreateInputsModel.GRiwrm.Rd | 66 ++++++++++++---
man/CreateInputsModel.Rd | 3 +
man/CreateInputsModel.default.Rd | 16 ----
man/CreateRunOptions.Rd | 83 +++++++++++++------
man/CreateSupervisor.Rd | 1 -
man/RunModel.GR.Rd | 43 +---------
man/RunModel.GRiwrmInputsModel.Rd | 65 ++++++++++-----
man/plot.GRiwrmOutputsModel.Rd | 65 ++++++++++-----
tests/testthat/helper_RunModel.R | 2 +-
tests/testthat/helper_cemaneige.R | 2 -
tests/testthat/test-Calibration.R | 40 ++++++++-
tests/testthat/test-CreateCalibOptions.R | 6 ++
tests/testthat/test-CreateInputsCrit.R | 31 +++++++
tests/testthat/test-CreateInputsModel.R | 21 ++++-
tests/testthat/test-CreateRunOptions.R | 52 ++++++++++++
tests/testthat/test-RunModel.R | 28 ++++---
vignettes/V02_Calibration_SD_model.Rmd | 4 +-
vignettes/V03_Open-loop_influenced_flow.Rmd | 2 +-
.../V04_Closed-loop_regulated_withdrawal.Rmd | 2 +-
vignettes/seinebasin/V02_First_run.Rmd | 2 +-
.../seinebasin/V03_First_Calibration.Rmd | 2 +-
.../V04_Open-loop_influenced_flow.Rmd | 2 +-
..._Open-loop_influenced_flow_calibration.Rmd | 4 +-
...-loop_influenced_flow_calibration_GR6J.Rmd | 4 +-
.../V06_Naturalised_flow_simulation.Rmd | 2 +-
48 files changed, 615 insertions(+), 316 deletions(-)
delete mode 100644 R/CreateCalibOptions.InputsModel.R
delete mode 100644 R/CreateInputsModel.default.R
delete mode 100644 R/CreateRunOptions.InputsModel.R
create mode 100644 man-roxygen/param_x.R
delete mode 100644 man/CreateInputsModel.default.Rd
create mode 100644 tests/testthat/test-CreateCalibOptions.R
create mode 100644 tests/testthat/test-CreateRunOptions.R
diff --git a/.Rbuildignore b/.Rbuildignore
index 911f877..03fd9b3 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -11,3 +11,4 @@
^pkgdown
^docs
^vignettes/seinebasin$
+^man-roxygen$
diff --git a/DESCRIPTION b/DESCRIPTION
index 437b90a..bb1ee74 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -16,8 +16,7 @@ Imports:
dplyr,
utils,
grDevices,
- graphics,
- airGR (>= 1.6.12.9001)
+ graphics
Suggests:
knitr,
rmarkdown,
@@ -29,6 +28,7 @@ VignetteBuilder: knitr
URL: https://airgriwrm.g-eau.fr/
BugReports: https://gitlab.irstea.fr/in-wop/airGRiwrm/-/issues/
Depends:
- R (>= 2.10)
+ R (>= 2.10),
+ airGR (>= 1.6.12.9001)
Remotes:
url::https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/archive/dev/airgr-dev.zip
diff --git a/NAMESPACE b/NAMESPACE
index ac8670f..2117129 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,14 +5,18 @@ S3method(Calibration,InputsModel)
S3method(ConvertMeteoSD,GRiwrm)
S3method(ConvertMeteoSD,character)
S3method(ConvertMeteoSD,matrix)
+S3method(CreateCalibOptions,"function")
S3method(CreateCalibOptions,GRiwrmInputsModel)
S3method(CreateCalibOptions,InputsModel)
+S3method(CreateCalibOptions,character)
S3method(CreateInputsCrit,GRiwrmInputsModel)
S3method(CreateInputsCrit,InputsModel)
S3method(CreateInputsModel,GRiwrm)
S3method(CreateInputsModel,default)
+S3method(CreateRunOptions,"function")
S3method(CreateRunOptions,GRiwrmInputsModel)
S3method(CreateRunOptions,InputsModel)
+S3method(CreateRunOptions,character)
S3method(RunModel,GR)
S3method(RunModel,GRiwrmInputsModel)
S3method(RunModel,InputsModel)
diff --git a/R/Calibration.GRiwrmInputsModel.R b/R/Calibration.GRiwrmInputsModel.R
index af28833..1199a98 100644
--- a/R/Calibration.GRiwrmInputsModel.R
+++ b/R/Calibration.GRiwrmInputsModel.R
@@ -78,6 +78,7 @@ Calibration.GRiwrmInputsModel <- function(InputsModel,
#' @param InputsCrit \[InputsCritLavenneFunction\] object internally created by [CreateInputsCrit.GRiwrmInputsModel]
#'
#' @return \[InputsCrit\] object with De Lavenne regularisation
+#' @import airGR
#' @noRd
#'
getInputsCrit_Lavenne <- function(id, OutputsModel, InputsCrit) {
diff --git a/R/Calibration.InputsModel.R b/R/Calibration.InputsModel.R
index e030148..1b5fba1 100644
--- a/R/Calibration.InputsModel.R
+++ b/R/Calibration.InputsModel.R
@@ -1,5 +1,9 @@
#' @rdname Calibration
#' @export
Calibration.InputsModel <- function(InputsModel, ...) {
- airGR::Calibration(InputsModel, FUN_MOD = InputsModel$FUN_MOD, ...)
+ if (!exists("FUN_MOD") && !is.null(InputsModel$FUN_MOD)) {
+ airGR::Calibration(InputsModel, FUN_MOD = InputsModel$FUN_MOD, ...)
+ } else {
+ airGR::Calibration(InputsModel, ...)
+ }
}
diff --git a/R/CreateCalibOptions.GRiwrmInputsModel.R b/R/CreateCalibOptions.GRiwrmInputsModel.R
index ffadd50..8abb580 100644
--- a/R/CreateCalibOptions.GRiwrmInputsModel.R
+++ b/R/CreateCalibOptions.GRiwrmInputsModel.R
@@ -1,13 +1,13 @@
#' @rdname CreateCalibOptions
#' @export
-CreateCalibOptions.GRiwrmInputsModel <- function(InputsModel, ...) {
+CreateCalibOptions.GRiwrmInputsModel <- function(x, ...) {
CalibOptions <- list()
class(CalibOptions) <- c("GRiwrmCalibOptions", class(CalibOptions))
- for(IM in InputsModel) {
- CalibOptions[[IM$id]] <- CreateCalibOptions.InputsModel(
- InputsModel = IM,
+ for(IM in x) {
+ CalibOptions[[IM$id]] <- CreateCalibOptions(
+ IM,
...
)
}
diff --git a/R/CreateCalibOptions.InputsModel.R b/R/CreateCalibOptions.InputsModel.R
deleted file mode 100644
index e1f139e..0000000
--- a/R/CreateCalibOptions.InputsModel.R
+++ /dev/null
@@ -1,10 +0,0 @@
-#' @rdname CreateCalibOptions
-#' @export
-CreateCalibOptions.InputsModel <- function(InputsModel,
- ...) {
- airGR::CreateCalibOptions(
- FUN_MOD = InputsModel$FUN_MOD,
- IsSD = !is.null(InputsModel$Qupstream),
- ...
- )
-}
diff --git a/R/CreateCalibOptions.R b/R/CreateCalibOptions.R
index ddef1e8..8c65ecf 100644
--- a/R/CreateCalibOptions.R
+++ b/R/CreateCalibOptions.R
@@ -2,7 +2,7 @@
#'
#' This function can be used either for a catchment (with an \emph{InputsModel} object) or for a network (with a \emph{GRiwrmInputsModel} object)
#'
-#' @param InputsModel object of class \emph{InputsModel} or \emph{GRiwrmInputsModel}. See [CreateInputsModel] for details
+#' @template param_x
#' @param ... arguments passed to [airGR::CreateCalibOptions], see details
#'
#' @details See [airGR::CreateCalibOptions] documentation for a complete list of arguments.
@@ -15,6 +15,43 @@
#'
#' @rdname CreateCalibOptions
#' @export
-CreateCalibOptions <- function(InputsModel, ...) {
- UseMethod("CreateCalibOptions", InputsModel)
+CreateCalibOptions <- function(x, ...) {
+ UseMethod("CreateCalibOptions", x)
+}
+
+#' @rdname CreateCalibOptions
+#' @export
+CreateCalibOptions.InputsModel <- function(x,
+ ...) {
+ if (!exists("FUN_MOD") && !is.null(x$FUN_MOD)) {
+ airGR::CreateCalibOptions(
+ FUN_MOD = x$FUN_MOD,
+ IsSD = !is.null(x$Qupstream),
+ ...
+ )
+ } else {
+ airGR::CreateCalibOptions(
+ ...
+ )
+ }
+}
+
+#' @rdname CreateCalibOptions
+#' @export
+CreateCalibOptions.character <- function(x,
+ ...) {
+ airGR::CreateCalibOptions(
+ FUN_MOD = x,
+ ...
+ )
+}
+
+#' @rdname CreateCalibOptions
+#' @export
+CreateCalibOptions.function <- function(x,
+ ...) {
+ airGR::CreateCalibOptions(
+ FUN_MOD = x,
+ ...
+ )
}
diff --git a/R/CreateGRiwrm.R b/R/CreateGRiwrm.R
index 6386b07..69f704b 100644
--- a/R/CreateGRiwrm.R
+++ b/R/CreateGRiwrm.R
@@ -21,28 +21,7 @@
#'
#' @aliases GRiwrm
#' @export
-#' @examples
-#' ###################################################################
-#' # Run the `airGR::RunModel_Lag` example in the GRiwrm fashion way #
-#' ###################################################################
-#'
-#' # Run the airGR RunModel_Lag example for harvesting the necessary data
-#' library(airGR)
-#' example(RunModel_Lag)
-#' # detach the package because otherwise airGR overwrites the airGRiwrm functions
-#' detach("package:airGR")
-#'
-#' # This example is a network of 2 nodes which can be described like this:
-#' db <- data.frame(id = c("Reservoir", "GaugingDown"),
-#' length = c(LengthHydro, NA),
-#' down = c("GaugingDown", NA),
-#' area = c(NA, BasinInfo$BasinArea),
-#' model = c(NA, "RunModel_GR4J"),
-#' stringsAsFactors = FALSE)
-#'
-#' # Create GRiwrm object from the data.frame
-#' griwrm <- CreateGRiwrm(db)
-#' str(griwrm)
+#' @inherit RunModel.GRiwrmInputsModel return examples
#'
CreateGRiwrm <- function(db,
cols = list(
diff --git a/R/CreateInputsCrit.GRiwrmInputsModel.R b/R/CreateInputsCrit.GRiwrmInputsModel.R
index d91ac39..e27db7b 100644
--- a/R/CreateInputsCrit.GRiwrmInputsModel.R
+++ b/R/CreateInputsCrit.GRiwrmInputsModel.R
@@ -1,7 +1,8 @@
#' @rdname CreateInputsCrit
+#' @import airGR
#' @export
CreateInputsCrit.GRiwrmInputsModel <- function(InputsModel,
- FUN_CRIT = airGR::ErrorCrit_NSE,
+ FUN_CRIT = ErrorCrit_NSE,
RunOptions,
Obs,
AprioriIds = NULL,
diff --git a/R/CreateInputsModel.GRiwrm.R b/R/CreateInputsModel.GRiwrm.R
index d780b6b..17bb6d1 100644
--- a/R/CreateInputsModel.GRiwrm.R
+++ b/R/CreateInputsModel.GRiwrm.R
@@ -20,47 +20,7 @@
#'
#' @return A \emph{GRiwrmInputsModel} object which is a list of \emph{InputsModel} objects created by [airGR::CreateInputsModel] with one item per modelled sub-catchment.
#' @export
-#' @examples
-#' ##################################################################
-#' # Run the `airGR RunModel_Lag` example in the GRiwrm fashion way #
-#' ##################################################################
-#'
-#' # Run the airGR RunModel_Lag example for harvesting necessary data
-#' library(airGR)
-#' example(RunModel_Lag)
-#' # detach the package because otherwise airGR overwrites the airGRiwrm functions
-#' detach("package:airGR")
-#'
-#' # This example is a network of 2 nodes which can be described like this:
-#' db <- data.frame(id = c("Reservoir", "GaugingDown"),
-#' length = c(LengthHydro, NA),
-#' down = c("GaugingDown", NA),
-#' area = c(NA, BasinInfo$BasinArea),
-#' model = c(NA, "RunModel_GR4J"),
-#' stringsAsFactors = FALSE)
-#'
-#' # Create GRiwrm object from the data.frame
-#' griwrm <- CreateGRiwrm(db)
-#' str(griwrm)
-#'
-#' # Formatting observations for the hydrological models
-#' # Each input data should be a matrix or a data.frame with the correct id as the column name
-#' Precip <- matrix(BasinObs$P, ncol = 1)
-#' colnames(Precip) <- "GaugingDown"
-#' PotEvap <- matrix(BasinObs$E, ncol = 1)
-#' colnames(PotEvap) <- "GaugingDown"
-#'
-#' # Observed flows should at least contains flows that are directly injected in the model
-#' Qobs = matrix(Qupstream, ncol = 1)
-#' colnames(Qobs) <- "Reservoir"
-#' str(Qobs)
-#'
-#' InputsModels <- CreateInputsModel(griwrm,
-#' DatesR = BasinObs$DatesR,
-#' Precip = Precip,
-#' PotEvap = PotEvap,
-#' Qobs = Qobs)
-#' str(InputsModels)
+#' @inherit RunModel.GRiwrmInputsModel return examples
#'
CreateInputsModel.GRiwrm <- function(x, DatesR,
Precip = NULL,
diff --git a/R/CreateInputsModel.R b/R/CreateInputsModel.R
index 6d17dda..f034cc1 100644
--- a/R/CreateInputsModel.R
+++ b/R/CreateInputsModel.R
@@ -6,7 +6,17 @@
#' @param ... further arguments passed to or from other methods.
#'
#' @return InputsModel or GRiwrmInputsObject object
+#' @rdname CreateInputsModel
+#' @import airGR
#' @export
CreateInputsModel <- function(x, ...) {
UseMethod("CreateInputsModel", x)
}
+
+#' @rdname CreateInputsModel
+#' @export
+CreateInputsModel.default <- function(x,
+ ...) {
+
+ airGR::CreateInputsModel(FUN_MOD = x, ...)
+}
diff --git a/R/CreateInputsModel.default.R b/R/CreateInputsModel.default.R
deleted file mode 100644
index eaca56b..0000000
--- a/R/CreateInputsModel.default.R
+++ /dev/null
@@ -1,12 +0,0 @@
-#' Wrapper for [airGR::CreateInputsModel] for one sub-basin
-#'
-#' @param x [function] hydrological model function (e.g. [airGR::RunModel_GR4J]...)
-#' @param ... arguments passed to [airGR::CreateInputsModel]
-#' @import airGR
-#' @export
-#'
-CreateInputsModel.default <- function(x,
- ...) {
-
- airGR::CreateInputsModel(FUN_MOD = x, ...)
-}
diff --git a/R/CreateRunOptions.GRiwrmInputsModel.R b/R/CreateRunOptions.GRiwrmInputsModel.R
index 637b58f..e7f503c 100644
--- a/R/CreateRunOptions.GRiwrmInputsModel.R
+++ b/R/CreateRunOptions.GRiwrmInputsModel.R
@@ -1,13 +1,13 @@
#' @param IniStates (optional) [numeric] object or [list] of [numeric] object of class \emph{IniStates}, see [airGR::CreateIniStates] for details
#' @rdname CreateRunOptions
#' @export
-CreateRunOptions.GRiwrmInputsModel <- function(InputsModel, IniStates = NULL, ...) {
+CreateRunOptions.GRiwrmInputsModel <- function(x, IniStates = NULL, ...) {
RunOptions <- list()
class(RunOptions) <- append(class(RunOptions), "GRiwrmRunOptions")
- for(id in names(InputsModel)) {
- RunOptions[[id]] <- CreateRunOptions(InputsModel = InputsModel[[id]], IniStates = IniStates[[id]], ...)
+ for(id in names(x)) {
+ RunOptions[[id]] <- CreateRunOptions(x[[id]], IniStates = IniStates[[id]], ...)
}
return(RunOptions)
}
diff --git a/R/CreateRunOptions.InputsModel.R b/R/CreateRunOptions.InputsModel.R
deleted file mode 100644
index bb0f2e7..0000000
--- a/R/CreateRunOptions.InputsModel.R
+++ /dev/null
@@ -1,8 +0,0 @@
-#' @rdname CreateRunOptions
-#' @export
-CreateRunOptions.InputsModel <- function(InputsModel, ...) {
-
- airGR::CreateRunOptions(FUN_MOD = InputsModel$FUN_MOD,
- InputsModel = InputsModel,
- ...)
-}
diff --git a/R/CreateRunOptions.R b/R/CreateRunOptions.R
index a0d4753..21d47a7 100644
--- a/R/CreateRunOptions.R
+++ b/R/CreateRunOptions.R
@@ -2,7 +2,7 @@
#'
#' This function can be used either for a catchment (with an \emph{InputsModel} object) or for a network (with a \emph{GRiwrmInputsModel} object)
#'
-#' @param InputsModel object of class \emph{InputsModel} or \emph{GRiwrmInputsModel}. See [CreateInputsModel] for details
+#' @template param_x
#' @param ... arguments passed to [airGR::CreateRunOptions], see details
#'
#' @details See [airGR::CreateRunOptions] documentation for a complete list of arguments.
@@ -18,6 +18,35 @@
#' @rdname CreateRunOptions
#' @export
#' @inherit RunModel.GRiwrmInputsModel return examples
-CreateRunOptions <- function(InputsModel, ...) {
- UseMethod("CreateRunOptions", InputsModel)
+CreateRunOptions <- function(x, ...) {
+ UseMethod("CreateRunOptions", x)
+}
+
+#' @rdname CreateRunOptions
+#' @export
+CreateRunOptions.InputsModel <- function(x, ...) {
+ if (!exists("FUN_MOD") && !is.null(x$FUN_MOD)) {
+ airGR::CreateRunOptions(FUN_MOD = x$FUN_MOD,
+ InputsModel = x,
+ ...)
+ } else {
+ airGR::CreateRunOptions(InputsModel = x,
+ ...)
+ }
+}
+
+#' @rdname CreateRunOptions
+#' @export
+CreateRunOptions.character <- function(x, ...) {
+
+ airGR::CreateRunOptions(FUN_MOD = x,
+ ...)
+}
+
+#' @rdname CreateRunOptions
+#' @export
+CreateRunOptions.function <- function(x, ...) {
+
+ airGR::CreateRunOptions(FUN_MOD = x,
+ ...)
}
diff --git a/R/CreateSupervisor.R b/R/CreateSupervisor.R
index 06de63a..3a6b109 100644
--- a/R/CreateSupervisor.R
+++ b/R/CreateSupervisor.R
@@ -14,7 +14,6 @@
#' @examples
#' data(Severn)
#' nodes <- Severn$BasinsInfo[, c("gauge_id", "downstream_id", "distance_downstream", "area")]
-#' nodes$distance_downstream <- nodes$distance_downstream * 1000 # Conversion km -> m
#' nodes$model <- "RunModel_GR4J"
#' griwrm <- CreateGRiwrm(nodes,
#' list(id = "gauge_id",
diff --git a/R/RunModel.GR.R b/R/RunModel.GR.R
index 7f708e8..b34a7ba 100644
--- a/R/RunModel.GR.R
+++ b/R/RunModel.GR.R
@@ -1,9 +1,11 @@
#' Run of a rainfall-runoff model on a sub-basin
#'
-#' @inherit airGR::RunModel
#' @param x \[object of class `InputsModel`\] `InputsModel` for [airGR::RunModel]
+#' @param RunOptions \[object of class *RunOptions*\] see [airGR::CreateRunOptions] for details
+#' @param Param [numeric] vector of model parameters (See details for SD lag model)
#' @param ... further arguments passed to or from other methods
#'
+#' @inherit airGR::RunModel description details return
#' @export
#'
RunModel.GR <- function(x, RunOptions, Param, ...) {
diff --git a/R/RunModel.GRiwrmInputsModel.R b/R/RunModel.GRiwrmInputsModel.R
index 0b3df93..01d7f3d 100644
--- a/R/RunModel.GRiwrmInputsModel.R
+++ b/R/RunModel.GRiwrmInputsModel.R
@@ -8,15 +8,36 @@
#' @return [[list] of class \emph{GRiwrmOutputsModel}] list of \emph{OutputsModel} objects (See \[airGR::RunModel]) for each node of the semi-distributed model
#' @export
#' @examples
-#' #################################################################
-#' # Run the `airGRRunModel_Lag` example in the GRiwrm fashion way #
-#' #################################################################
+#' ###################################################################
+#' # Run the `airGR::RunModel_Lag` example in the GRiwrm fashion way #
+#' # Simulation of a reservoir with a purpose of low-flow mitigation #
+#' ###################################################################
#'
-#' # Run the airGR RunModel_Lag example for harvesting necessary data
-#' library(airGR)
-#' example(RunModel_Lag)
-#' # detach the package because otherwise airGR overwrites the airGRiwrm functions
-#' detach("package:airGR")
+#' ## ---- preparation of the InputsModel object
+#'
+#' ## loading package and catchment data
+#' library(airGRiwrm)
+#' data(L0123001)
+#'
+#' ## ---- specifications of the reservoir
+#'
+#' ## the reservoir withdraws 1 m3/s when it's possible considering the flow observed in the basin
+#' Qupstream <- matrix(-sapply(BasinObs$Qls / 1000 - 1, function(x) {
+#' min(1, max(0, x, na.rm = TRUE))
+#' }), ncol = 1)
+#'
+#' ## except between July and September when the reservoir releases 3 m3/s for low-flow mitigation
+#' month <- as.numeric(format(BasinObs$DatesR, "%m"))
+#' Qupstream[month >= 7 & month <= 9] <- 3
+#' Qupstream <- Qupstream * 86400 ## Conversion in m3/day
+#'
+#' ## the reservoir is not an upstream subcachment: its areas is NA
+#' BasinAreas <- c(NA, BasinInfo$BasinArea)
+#'
+#' ## delay time between the reservoir and the catchment outlet is 2 days and the distance is 150 km
+#' LengthHydro <- 150
+#' ## with a delay of 2 days for 150 km, the flow velocity is 75 km per day
+#' Velocity <- (LengthHydro * 1e3 / 2) / (24 * 60 * 60) ## Conversion km/day -> m/s
#'
#' # This example is a network of 2 nodes which can be describe like this:
#' db <- data.frame(id = c("Reservoir", "GaugingDown"),
@@ -37,12 +58,9 @@
#' PotEvap <- matrix(BasinObs$E, ncol = 1)
#' colnames(PotEvap) <- "GaugingDown"
#'
-#' # Observed flows are integrated now because we mix:
-#' # - flows that are directly injected in the model
-#' # - flows that could be used for the calibration of the hydrological models
-#' Qobs = matrix(c(Qupstream, BasinObs$Qmm), ncol = 2)
-#' colnames(Qobs) <- griwrm$id
-#' str(Qobs)
+#' # Observed flows contain flows that are directly injected in the model
+#' Qobs = matrix(Qupstream, ncol = 1)
+#' colnames(Qobs) <- "Reservoir"
#'
#' # Creation of the GRiwrmInputsModel object (= a named list of InputsModel objects)
#' InputsModels <- CreateInputsModel(griwrm,
@@ -52,22 +70,27 @@
#' Qobs = Qobs)
#' str(InputsModels)
#'
+#' ## run period selection
+#' Ind_Run <- seq(which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1990-01-01"),
+#' which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1999-12-31"))
+#'
#' # Creation of the GriwmRunOptions object
-#' RunOptions2 <- CreateRunOptions(InputsModels,
+#' RunOptions <- CreateRunOptions(InputsModels,
#' IndPeriod_Run = Ind_Run)
-#' str(RunOptions2)
+#' str(RunOptions)
#'
#' # Parameters of the SD models should be encapsulated in a named list
-#' Param2 <- list(`GaugingDown` = c(Velocity, Param))
+#' ParamGR4J <- c(X1 = 257.238, X2 = 1.012, X3 = 88.235, X4 = 2.208)
+#' Param <- list(`GaugingDown` = c(Velocity, ParamGR4J))
#'
#' # RunModel for the whole network
#' OutputsModels <- RunModel(InputsModels,
-#' RunOptions = RunOptions2,
-#' Param = Param2)
+#' RunOptions = RunOptions,
+#' Param = Param)
#' str(OutputsModels)
#'
-#' # Comparison between GRiwrm simulation and airGR simulation
-#' plot(OutputsModels, Qobs = data.frame(`GaugingDown` = OutputsModel$Qsim))
+#' # Compare Simulation with reservoir and observation of natural flow
+#' plot(OutputsModels, data.frame(GaugingDown = BasinObs$Qmm[Ind_Run]))
RunModel.GRiwrmInputsModel <- function(x, RunOptions, Param, ...) {
checkRunModelParameters(x, RunOptions, Param)
diff --git a/man-roxygen/param_x.R b/man-roxygen/param_x.R
new file mode 100644
index 0000000..0e25a80
--- /dev/null
+++ b/man-roxygen/param_x.R
@@ -0,0 +1,2 @@
+#' @param x [function], [character], or object of class \emph{InputsModel} runs [airGR::CreateRunOptions]for a catchment. Use object of class \emph{GRiwrmInputsModel} for a network. See [CreateInputsModel] for details
+#'
diff --git a/man/CreateCalibOptions.Rd b/man/CreateCalibOptions.Rd
index c2a2e13..74b6eb7 100644
--- a/man/CreateCalibOptions.Rd
+++ b/man/CreateCalibOptions.Rd
@@ -1,20 +1,26 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/CreateCalibOptions.GRiwrmInputsModel.R,
-% R/CreateCalibOptions.InputsModel.R, R/CreateCalibOptions.R
+% R/CreateCalibOptions.R
\name{CreateCalibOptions.GRiwrmInputsModel}
\alias{CreateCalibOptions.GRiwrmInputsModel}
-\alias{CreateCalibOptions.InputsModel}
\alias{CreateCalibOptions}
+\alias{CreateCalibOptions.InputsModel}
+\alias{CreateCalibOptions.character}
+\alias{CreateCalibOptions.function}
\title{Creation of the CalibOptions object}
\usage{
-\method{CreateCalibOptions}{GRiwrmInputsModel}(InputsModel, ...)
+\method{CreateCalibOptions}{GRiwrmInputsModel}(x, ...)
+
+CreateCalibOptions(x, ...)
+
+\method{CreateCalibOptions}{InputsModel}(x, ...)
-\method{CreateCalibOptions}{InputsModel}(InputsModel, ...)
+\method{CreateCalibOptions}{character}(x, ...)
-CreateCalibOptions(InputsModel, ...)
+\method{CreateCalibOptions}{`function`}(x, ...)
}
\arguments{
-\item{InputsModel}{object of class \emph{InputsModel} or \emph{GRiwrmInputsModel}. See \link{CreateInputsModel} for details}
+\item{x}{\link{function}, \link{character}, or object of class \emph{InputsModel} runs \link[airGR:CreateRunOptions]{airGR::CreateRunOptions}for a catchment. Use object of class \emph{GRiwrmInputsModel} for a network. See \link{CreateInputsModel} for details}
\item{...}{arguments passed to \link[airGR:CreateCalibOptions]{airGR::CreateCalibOptions}, see details}
}
diff --git a/man/CreateGRiwrm.Rd b/man/CreateGRiwrm.Rd
index f962ec2..ab1ad35 100644
--- a/man/CreateGRiwrm.Rd
+++ b/man/CreateGRiwrm.Rd
@@ -46,15 +46,36 @@ of their connections
\examples{
###################################################################
# Run the `airGR::RunModel_Lag` example in the GRiwrm fashion way #
+# Simulation of a reservoir with a purpose of low-flow mitigation #
###################################################################
-# Run the airGR RunModel_Lag example for harvesting the necessary data
-library(airGR)
-example(RunModel_Lag)
-# detach the package because otherwise airGR overwrites the airGRiwrm functions
-detach("package:airGR")
+## ---- preparation of the InputsModel object
-# This example is a network of 2 nodes which can be described like this:
+## loading package and catchment data
+library(airGRiwrm)
+data(L0123001)
+
+## ---- specifications of the reservoir
+
+## the reservoir withdraws 1 m3/s when it's possible considering the flow observed in the basin
+Qupstream <- matrix(-sapply(BasinObs$Qls / 1000 - 1, function(x) {
+ min(1, max(0, x, na.rm = TRUE))
+}), ncol = 1)
+
+## except between July and September when the reservoir releases 3 m3/s for low-flow mitigation
+month <- as.numeric(format(BasinObs$DatesR, "\%m"))
+Qupstream[month >= 7 & month <= 9] <- 3
+Qupstream <- Qupstream * 86400 ## Conversion in m3/day
+
+## the reservoir is not an upstream subcachment: its areas is NA
+BasinAreas <- c(NA, BasinInfo$BasinArea)
+
+## delay time between the reservoir and the catchment outlet is 2 days and the distance is 150 km
+LengthHydro <- 150
+## with a delay of 2 days for 150 km, the flow velocity is 75 km per day
+Velocity <- (LengthHydro * 1e3 / 2) / (24 * 60 * 60) ## Conversion km/day -> m/s
+
+# This example is a network of 2 nodes which can be describe like this:
db <- data.frame(id = c("Reservoir", "GaugingDown"),
length = c(LengthHydro, NA),
down = c("GaugingDown", NA),
@@ -66,4 +87,44 @@ db <- data.frame(id = c("Reservoir", "GaugingDown"),
griwrm <- CreateGRiwrm(db)
str(griwrm)
+# Formatting observations for the hydrological models
+# Each input data should be a matrix or a data.frame with the good id in the name of the column
+Precip <- matrix(BasinObs$P, ncol = 1)
+colnames(Precip) <- "GaugingDown"
+PotEvap <- matrix(BasinObs$E, ncol = 1)
+colnames(PotEvap) <- "GaugingDown"
+
+# Observed flows contain flows that are directly injected in the model
+Qobs = matrix(Qupstream, ncol = 1)
+colnames(Qobs) <- "Reservoir"
+
+# Creation of the GRiwrmInputsModel object (= a named list of InputsModel objects)
+InputsModels <- CreateInputsModel(griwrm,
+ DatesR = BasinObs$DatesR,
+ Precip = Precip,
+ PotEvap = PotEvap,
+ Qobs = Qobs)
+str(InputsModels)
+
+## run period selection
+Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
+ which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
+
+# Creation of the GriwmRunOptions object
+RunOptions <- CreateRunOptions(InputsModels,
+ IndPeriod_Run = Ind_Run)
+str(RunOptions)
+
+# Parameters of the SD models should be encapsulated in a named list
+ParamGR4J <- c(X1 = 257.238, X2 = 1.012, X3 = 88.235, X4 = 2.208)
+Param <- list(`GaugingDown` = c(Velocity, ParamGR4J))
+
+# RunModel for the whole network
+OutputsModels <- RunModel(InputsModels,
+ RunOptions = RunOptions,
+ Param = Param)
+str(OutputsModels)
+
+# Compare Simulation with reservoir and observation of natural flow
+plot(OutputsModels, data.frame(GaugingDown = BasinObs$Qmm[Ind_Run]))
}
diff --git a/man/CreateInputsCrit.Rd b/man/CreateInputsCrit.Rd
index dcfdeee..3ec30d5 100644
--- a/man/CreateInputsCrit.Rd
+++ b/man/CreateInputsCrit.Rd
@@ -9,7 +9,7 @@
\usage{
\method{CreateInputsCrit}{GRiwrmInputsModel}(
InputsModel,
- FUN_CRIT = airGR::ErrorCrit_NSE,
+ FUN_CRIT = ErrorCrit_NSE,
RunOptions,
Obs,
AprioriIds = NULL,
diff --git a/man/CreateInputsModel.GRiwrm.Rd b/man/CreateInputsModel.GRiwrm.Rd
index c442d6d..fe944a4 100644
--- a/man/CreateInputsModel.GRiwrm.Rd
+++ b/man/CreateInputsModel.GRiwrm.Rd
@@ -59,17 +59,38 @@ Meteorological data are needed for the nodes of the network that represent a cat
See \link[airGR:CreateInputsModel]{airGR::CreateInputsModel} documentation for details concerning each input.
}
\examples{
-##################################################################
-# Run the `airGR RunModel_Lag` example in the GRiwrm fashion way #
-##################################################################
+###################################################################
+# Run the `airGR::RunModel_Lag` example in the GRiwrm fashion way #
+# Simulation of a reservoir with a purpose of low-flow mitigation #
+###################################################################
-# Run the airGR RunModel_Lag example for harvesting necessary data
-library(airGR)
-example(RunModel_Lag)
-# detach the package because otherwise airGR overwrites the airGRiwrm functions
-detach("package:airGR")
+## ---- preparation of the InputsModel object
-# This example is a network of 2 nodes which can be described like this:
+## loading package and catchment data
+library(airGRiwrm)
+data(L0123001)
+
+## ---- specifications of the reservoir
+
+## the reservoir withdraws 1 m3/s when it's possible considering the flow observed in the basin
+Qupstream <- matrix(-sapply(BasinObs$Qls / 1000 - 1, function(x) {
+ min(1, max(0, x, na.rm = TRUE))
+}), ncol = 1)
+
+## except between July and September when the reservoir releases 3 m3/s for low-flow mitigation
+month <- as.numeric(format(BasinObs$DatesR, "\%m"))
+Qupstream[month >= 7 & month <= 9] <- 3
+Qupstream <- Qupstream * 86400 ## Conversion in m3/day
+
+## the reservoir is not an upstream subcachment: its areas is NA
+BasinAreas <- c(NA, BasinInfo$BasinArea)
+
+## delay time between the reservoir and the catchment outlet is 2 days and the distance is 150 km
+LengthHydro <- 150
+## with a delay of 2 days for 150 km, the flow velocity is 75 km per day
+Velocity <- (LengthHydro * 1e3 / 2) / (24 * 60 * 60) ## Conversion km/day -> m/s
+
+# This example is a network of 2 nodes which can be describe like this:
db <- data.frame(id = c("Reservoir", "GaugingDown"),
length = c(LengthHydro, NA),
down = c("GaugingDown", NA),
@@ -82,17 +103,17 @@ griwrm <- CreateGRiwrm(db)
str(griwrm)
# Formatting observations for the hydrological models
-# Each input data should be a matrix or a data.frame with the correct id as the column name
+# Each input data should be a matrix or a data.frame with the good id in the name of the column
Precip <- matrix(BasinObs$P, ncol = 1)
colnames(Precip) <- "GaugingDown"
PotEvap <- matrix(BasinObs$E, ncol = 1)
colnames(PotEvap) <- "GaugingDown"
-# Observed flows should at least contains flows that are directly injected in the model
+# Observed flows contain flows that are directly injected in the model
Qobs = matrix(Qupstream, ncol = 1)
colnames(Qobs) <- "Reservoir"
-str(Qobs)
+# Creation of the GRiwrmInputsModel object (= a named list of InputsModel objects)
InputsModels <- CreateInputsModel(griwrm,
DatesR = BasinObs$DatesR,
Precip = Precip,
@@ -100,4 +121,25 @@ InputsModels <- CreateInputsModel(griwrm,
Qobs = Qobs)
str(InputsModels)
+## run period selection
+Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
+ which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
+
+# Creation of the GriwmRunOptions object
+RunOptions <- CreateRunOptions(InputsModels,
+ IndPeriod_Run = Ind_Run)
+str(RunOptions)
+
+# Parameters of the SD models should be encapsulated in a named list
+ParamGR4J <- c(X1 = 257.238, X2 = 1.012, X3 = 88.235, X4 = 2.208)
+Param <- list(`GaugingDown` = c(Velocity, ParamGR4J))
+
+# RunModel for the whole network
+OutputsModels <- RunModel(InputsModels,
+ RunOptions = RunOptions,
+ Param = Param)
+str(OutputsModels)
+
+# Compare Simulation with reservoir and observation of natural flow
+plot(OutputsModels, data.frame(GaugingDown = BasinObs$Qmm[Ind_Run]))
}
diff --git a/man/CreateInputsModel.Rd b/man/CreateInputsModel.Rd
index 213f986..39521c8 100644
--- a/man/CreateInputsModel.Rd
+++ b/man/CreateInputsModel.Rd
@@ -2,9 +2,12 @@
% Please edit documentation in R/CreateInputsModel.R
\name{CreateInputsModel}
\alias{CreateInputsModel}
+\alias{CreateInputsModel.default}
\title{Generic function for creating \code{InputsModel} object for either \strong{airGR} or \strong{airGRiwrm}}
\usage{
CreateInputsModel(x, ...)
+
+\method{CreateInputsModel}{default}(x, ...)
}
\arguments{
\item{x}{First parameter determining which InputsModel object is created}
diff --git a/man/CreateInputsModel.default.Rd b/man/CreateInputsModel.default.Rd
deleted file mode 100644
index ea83bb7..0000000
--- a/man/CreateInputsModel.default.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CreateInputsModel.default.R
-\name{CreateInputsModel.default}
-\alias{CreateInputsModel.default}
-\title{Wrapper for \link[airGR:CreateInputsModel]{airGR::CreateInputsModel} for one sub-basin}
-\usage{
-\method{CreateInputsModel}{default}(x, ...)
-}
-\arguments{
-\item{x}{\link{function} hydrological model function (e.g. \link[airGR:RunModel_GR4J]{airGR::RunModel_GR4J}...)}
-
-\item{...}{arguments passed to \link[airGR:CreateInputsModel]{airGR::CreateInputsModel}}
-}
-\description{
-Wrapper for \link[airGR:CreateInputsModel]{airGR::CreateInputsModel} for one sub-basin
-}
diff --git a/man/CreateRunOptions.Rd b/man/CreateRunOptions.Rd
index 36e6665..8f6bda1 100644
--- a/man/CreateRunOptions.Rd
+++ b/man/CreateRunOptions.Rd
@@ -1,20 +1,26 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/CreateRunOptions.GRiwrmInputsModel.R,
-% R/CreateRunOptions.InputsModel.R, R/CreateRunOptions.R
+% R/CreateRunOptions.R
\name{CreateRunOptions.GRiwrmInputsModel}
\alias{CreateRunOptions.GRiwrmInputsModel}
-\alias{CreateRunOptions.InputsModel}
\alias{CreateRunOptions}
+\alias{CreateRunOptions.InputsModel}
+\alias{CreateRunOptions.character}
+\alias{CreateRunOptions.function}
\title{Creation of the CalibOptions object}
\usage{
-\method{CreateRunOptions}{GRiwrmInputsModel}(InputsModel, IniStates = NULL, ...)
+\method{CreateRunOptions}{GRiwrmInputsModel}(x, IniStates = NULL, ...)
+
+CreateRunOptions(x, ...)
-\method{CreateRunOptions}{InputsModel}(InputsModel, ...)
+\method{CreateRunOptions}{InputsModel}(x, ...)
-CreateRunOptions(InputsModel, ...)
+\method{CreateRunOptions}{character}(x, ...)
+
+\method{CreateRunOptions}{`function`}(x, ...)
}
\arguments{
-\item{InputsModel}{object of class \emph{InputsModel} or \emph{GRiwrmInputsModel}. See \link{CreateInputsModel} for details}
+\item{x}{\link{function}, \link{character}, or object of class \emph{InputsModel} runs \link[airGR:CreateRunOptions]{airGR::CreateRunOptions}for a catchment. Use object of class \emph{GRiwrmInputsModel} for a network. See \link{CreateInputsModel} for details}
\item{IniStates}{(optional) \link{numeric} object or \link{list} of \link{numeric} object of class \emph{IniStates}, see \link[airGR:CreateIniStates]{airGR::CreateIniStates} for details}
@@ -38,15 +44,36 @@ If \code{InputsModel} argument is a \emph{GRiwrmInputsModel} object, \code{IniSt
With a \emph{GRiwrmInputsModel} object, all arguments are applied on each sub-catchments of the network.
}
\examples{
-#################################################################
-# Run the `airGRRunModel_Lag` example in the GRiwrm fashion way #
-#################################################################
+###################################################################
+# Run the `airGR::RunModel_Lag` example in the GRiwrm fashion way #
+# Simulation of a reservoir with a purpose of low-flow mitigation #
+###################################################################
+
+## ---- preparation of the InputsModel object
+
+## loading package and catchment data
+library(airGRiwrm)
+data(L0123001)
-# Run the airGR RunModel_Lag example for harvesting necessary data
-library(airGR)
-example(RunModel_Lag)
-# detach the package because otherwise airGR overwrites the airGRiwrm functions
-detach("package:airGR")
+## ---- specifications of the reservoir
+
+## the reservoir withdraws 1 m3/s when it's possible considering the flow observed in the basin
+Qupstream <- matrix(-sapply(BasinObs$Qls / 1000 - 1, function(x) {
+ min(1, max(0, x, na.rm = TRUE))
+}), ncol = 1)
+
+## except between July and September when the reservoir releases 3 m3/s for low-flow mitigation
+month <- as.numeric(format(BasinObs$DatesR, "\%m"))
+Qupstream[month >= 7 & month <= 9] <- 3
+Qupstream <- Qupstream * 86400 ## Conversion in m3/day
+
+## the reservoir is not an upstream subcachment: its areas is NA
+BasinAreas <- c(NA, BasinInfo$BasinArea)
+
+## delay time between the reservoir and the catchment outlet is 2 days and the distance is 150 km
+LengthHydro <- 150
+## with a delay of 2 days for 150 km, the flow velocity is 75 km per day
+Velocity <- (LengthHydro * 1e3 / 2) / (24 * 60 * 60) ## Conversion km/day -> m/s
# This example is a network of 2 nodes which can be describe like this:
db <- data.frame(id = c("Reservoir", "GaugingDown"),
@@ -67,12 +94,9 @@ colnames(Precip) <- "GaugingDown"
PotEvap <- matrix(BasinObs$E, ncol = 1)
colnames(PotEvap) <- "GaugingDown"
-# Observed flows are integrated now because we mix:
-# - flows that are directly injected in the model
-# - flows that could be used for the calibration of the hydrological models
-Qobs = matrix(c(Qupstream, BasinObs$Qmm), ncol = 2)
-colnames(Qobs) <- griwrm$id
-str(Qobs)
+# Observed flows contain flows that are directly injected in the model
+Qobs = matrix(Qupstream, ncol = 1)
+colnames(Qobs) <- "Reservoir"
# Creation of the GRiwrmInputsModel object (= a named list of InputsModel objects)
InputsModels <- CreateInputsModel(griwrm,
@@ -82,20 +106,25 @@ InputsModels <- CreateInputsModel(griwrm,
Qobs = Qobs)
str(InputsModels)
+## run period selection
+Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
+ which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
+
# Creation of the GriwmRunOptions object
-RunOptions2 <- CreateRunOptions(InputsModels,
+RunOptions <- CreateRunOptions(InputsModels,
IndPeriod_Run = Ind_Run)
-str(RunOptions2)
+str(RunOptions)
# Parameters of the SD models should be encapsulated in a named list
-Param2 <- list(`GaugingDown` = c(Velocity, Param))
+ParamGR4J <- c(X1 = 257.238, X2 = 1.012, X3 = 88.235, X4 = 2.208)
+Param <- list(`GaugingDown` = c(Velocity, ParamGR4J))
# RunModel for the whole network
OutputsModels <- RunModel(InputsModels,
- RunOptions = RunOptions2,
- Param = Param2)
+ RunOptions = RunOptions,
+ Param = Param)
str(OutputsModels)
-# Comparison between GRiwrm simulation and airGR simulation
-plot(OutputsModels, Qobs = data.frame(`GaugingDown` = OutputsModel$Qsim))
+# Compare Simulation with reservoir and observation of natural flow
+plot(OutputsModels, data.frame(GaugingDown = BasinObs$Qmm[Ind_Run]))
}
diff --git a/man/CreateSupervisor.Rd b/man/CreateSupervisor.Rd
index 6ada44b..e3c95b7 100644
--- a/man/CreateSupervisor.Rd
+++ b/man/CreateSupervisor.Rd
@@ -27,7 +27,6 @@ Creation of a Supervisor for handling regulation in a model
\examples{
data(Severn)
nodes <- Severn$BasinsInfo[, c("gauge_id", "downstream_id", "distance_downstream", "area")]
-nodes$distance_downstream <- nodes$distance_downstream * 1000 # Conversion km -> m
nodes$model <- "RunModel_GR4J"
griwrm <- CreateGRiwrm(nodes,
list(id = "gauge_id",
diff --git a/man/RunModel.GR.Rd b/man/RunModel.GR.Rd
index 1b76564..963391a 100644
--- a/man/RunModel.GR.Rd
+++ b/man/RunModel.GR.Rd
@@ -9,9 +9,9 @@
\arguments{
\item{x}{[object of class \code{InputsModel}] \code{InputsModel} for \link[airGR:RunModel]{airGR::RunModel}}
-\item{RunOptions}{[object of class \emph{RunOptions}] see \code{\link[airGR]{CreateRunOptions}} for details}
+\item{RunOptions}{[object of class \emph{RunOptions}] see \link[airGR:CreateRunOptions]{airGR::CreateRunOptions} for details}
-\item{Param}{[numeric] vector of model parameters (See details for SD lag model)}
+\item{Param}{\link{numeric} vector of model parameters (See details for SD lag model)}
\item{...}{further arguments passed to or from other methods}
}
@@ -26,42 +26,3 @@ Function which performs a single model run with the provided function over the s
\details{
If \code{InputsModel} parameter has been created for using a semi-distributed (SD) lag model (See \code{\link[airGR]{CreateInputsModel}}), the first item of \code{Param} parameter should contain a constant lag parameter expressed as a velocity in m/s, parameters for the hydrological model are then shift one position to the right.
}
-\examples{
-library(airGR)
-
-## loading catchment data
-data(L0123001)
-
-## preparation of the InputsModel object
-InputsModel <- CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR,
- Precip = BasinObs$P, PotEvap = BasinObs$E)
-
-## run period selection
-Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
- which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
-
-## preparation of the RunOptions object
-RunOptions <- CreateRunOptions(FUN_MOD = RunModel_GR4J,
- InputsModel = InputsModel, IndPeriod_Run = Ind_Run)
-
-## simulation
-Param <- c(X1 = 734.568, X2 = -0.840, X3 = 109.809, X4 = 1.971)
-OutputsModel <- RunModel(InputsModel = InputsModel,
- RunOptions = RunOptions, Param = Param,
- FUN_MOD = RunModel_GR4J)
-
-## results preview
-plot(OutputsModel, Qobs = BasinObs$Qmm[Ind_Run])
-
-## efficiency criterion: Nash-Sutcliffe Efficiency
-InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel,
- RunOptions = RunOptions, Obs = BasinObs$Qmm[Ind_Run])
-OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
-}
-\seealso{
-\code{\link[airGR]{RunModel_GR4J}}, \code{\link[airGR]{RunModel_CemaNeigeGR4J}}, \code{\link[airGR]{CreateInputsModel}},
-\code{\link[airGR]{CreateRunOptions}}, \code{\link[airGR]{CreateIniStates}}.
-}
-\author{
-Laurent Coron, Olivier Delaigue
-}
diff --git a/man/RunModel.GRiwrmInputsModel.Rd b/man/RunModel.GRiwrmInputsModel.Rd
index f5f614a..629450e 100644
--- a/man/RunModel.GRiwrmInputsModel.Rd
+++ b/man/RunModel.GRiwrmInputsModel.Rd
@@ -22,15 +22,36 @@
RunModel function for \emph{GRiwrmInputsModel} object
}
\examples{
-#################################################################
-# Run the `airGRRunModel_Lag` example in the GRiwrm fashion way #
-#################################################################
+###################################################################
+# Run the `airGR::RunModel_Lag` example in the GRiwrm fashion way #
+# Simulation of a reservoir with a purpose of low-flow mitigation #
+###################################################################
-# Run the airGR RunModel_Lag example for harvesting necessary data
-library(airGR)
-example(RunModel_Lag)
-# detach the package because otherwise airGR overwrites the airGRiwrm functions
-detach("package:airGR")
+## ---- preparation of the InputsModel object
+
+## loading package and catchment data
+library(airGRiwrm)
+data(L0123001)
+
+## ---- specifications of the reservoir
+
+## the reservoir withdraws 1 m3/s when it's possible considering the flow observed in the basin
+Qupstream <- matrix(-sapply(BasinObs$Qls / 1000 - 1, function(x) {
+ min(1, max(0, x, na.rm = TRUE))
+}), ncol = 1)
+
+## except between July and September when the reservoir releases 3 m3/s for low-flow mitigation
+month <- as.numeric(format(BasinObs$DatesR, "\%m"))
+Qupstream[month >= 7 & month <= 9] <- 3
+Qupstream <- Qupstream * 86400 ## Conversion in m3/day
+
+## the reservoir is not an upstream subcachment: its areas is NA
+BasinAreas <- c(NA, BasinInfo$BasinArea)
+
+## delay time between the reservoir and the catchment outlet is 2 days and the distance is 150 km
+LengthHydro <- 150
+## with a delay of 2 days for 150 km, the flow velocity is 75 km per day
+Velocity <- (LengthHydro * 1e3 / 2) / (24 * 60 * 60) ## Conversion km/day -> m/s
# This example is a network of 2 nodes which can be describe like this:
db <- data.frame(id = c("Reservoir", "GaugingDown"),
@@ -51,12 +72,9 @@ colnames(Precip) <- "GaugingDown"
PotEvap <- matrix(BasinObs$E, ncol = 1)
colnames(PotEvap) <- "GaugingDown"
-# Observed flows are integrated now because we mix:
-# - flows that are directly injected in the model
-# - flows that could be used for the calibration of the hydrological models
-Qobs = matrix(c(Qupstream, BasinObs$Qmm), ncol = 2)
-colnames(Qobs) <- griwrm$id
-str(Qobs)
+# Observed flows contain flows that are directly injected in the model
+Qobs = matrix(Qupstream, ncol = 1)
+colnames(Qobs) <- "Reservoir"
# Creation of the GRiwrmInputsModel object (= a named list of InputsModel objects)
InputsModels <- CreateInputsModel(griwrm,
@@ -66,20 +84,25 @@ InputsModels <- CreateInputsModel(griwrm,
Qobs = Qobs)
str(InputsModels)
+## run period selection
+Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
+ which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
+
# Creation of the GriwmRunOptions object
-RunOptions2 <- CreateRunOptions(InputsModels,
+RunOptions <- CreateRunOptions(InputsModels,
IndPeriod_Run = Ind_Run)
-str(RunOptions2)
+str(RunOptions)
# Parameters of the SD models should be encapsulated in a named list
-Param2 <- list(`GaugingDown` = c(Velocity, Param))
+ParamGR4J <- c(X1 = 257.238, X2 = 1.012, X3 = 88.235, X4 = 2.208)
+Param <- list(`GaugingDown` = c(Velocity, ParamGR4J))
# RunModel for the whole network
OutputsModels <- RunModel(InputsModels,
- RunOptions = RunOptions2,
- Param = Param2)
+ RunOptions = RunOptions,
+ Param = Param)
str(OutputsModels)
-# Comparison between GRiwrm simulation and airGR simulation
-plot(OutputsModels, Qobs = data.frame(`GaugingDown` = OutputsModel$Qsim))
+# Compare Simulation with reservoir and observation of natural flow
+plot(OutputsModels, data.frame(GaugingDown = BasinObs$Qmm[Ind_Run]))
}
diff --git a/man/plot.GRiwrmOutputsModel.Rd b/man/plot.GRiwrmOutputsModel.Rd
index 79d874a..42a99bf 100644
--- a/man/plot.GRiwrmOutputsModel.Rd
+++ b/man/plot.GRiwrmOutputsModel.Rd
@@ -22,15 +22,36 @@ by hydrological model output named with the node ID (See \link{CreateGRiwrm} for
Function which creates screen plots giving an overview of the model outputs in the GRiwrm network
}
\examples{
-#################################################################
-# Run the `airGRRunModel_Lag` example in the GRiwrm fashion way #
-#################################################################
+###################################################################
+# Run the `airGR::RunModel_Lag` example in the GRiwrm fashion way #
+# Simulation of a reservoir with a purpose of low-flow mitigation #
+###################################################################
-# Run the airGR RunModel_Lag example for harvesting necessary data
-library(airGR)
-example(RunModel_Lag)
-# detach the package because otherwise airGR overwrites the airGRiwrm functions
-detach("package:airGR")
+## ---- preparation of the InputsModel object
+
+## loading package and catchment data
+library(airGRiwrm)
+data(L0123001)
+
+## ---- specifications of the reservoir
+
+## the reservoir withdraws 1 m3/s when it's possible considering the flow observed in the basin
+Qupstream <- matrix(-sapply(BasinObs$Qls / 1000 - 1, function(x) {
+ min(1, max(0, x, na.rm = TRUE))
+}), ncol = 1)
+
+## except between July and September when the reservoir releases 3 m3/s for low-flow mitigation
+month <- as.numeric(format(BasinObs$DatesR, "\%m"))
+Qupstream[month >= 7 & month <= 9] <- 3
+Qupstream <- Qupstream * 86400 ## Conversion in m3/day
+
+## the reservoir is not an upstream subcachment: its areas is NA
+BasinAreas <- c(NA, BasinInfo$BasinArea)
+
+## delay time between the reservoir and the catchment outlet is 2 days and the distance is 150 km
+LengthHydro <- 150
+## with a delay of 2 days for 150 km, the flow velocity is 75 km per day
+Velocity <- (LengthHydro * 1e3 / 2) / (24 * 60 * 60) ## Conversion km/day -> m/s
# This example is a network of 2 nodes which can be describe like this:
db <- data.frame(id = c("Reservoir", "GaugingDown"),
@@ -51,12 +72,9 @@ colnames(Precip) <- "GaugingDown"
PotEvap <- matrix(BasinObs$E, ncol = 1)
colnames(PotEvap) <- "GaugingDown"
-# Observed flows are integrated now because we mix:
-# - flows that are directly injected in the model
-# - flows that could be used for the calibration of the hydrological models
-Qobs = matrix(c(Qupstream, BasinObs$Qmm), ncol = 2)
-colnames(Qobs) <- griwrm$id
-str(Qobs)
+# Observed flows contain flows that are directly injected in the model
+Qobs = matrix(Qupstream, ncol = 1)
+colnames(Qobs) <- "Reservoir"
# Creation of the GRiwrmInputsModel object (= a named list of InputsModel objects)
InputsModels <- CreateInputsModel(griwrm,
@@ -66,20 +84,25 @@ InputsModels <- CreateInputsModel(griwrm,
Qobs = Qobs)
str(InputsModels)
+## run period selection
+Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
+ which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
+
# Creation of the GriwmRunOptions object
-RunOptions2 <- CreateRunOptions(InputsModels,
+RunOptions <- CreateRunOptions(InputsModels,
IndPeriod_Run = Ind_Run)
-str(RunOptions2)
+str(RunOptions)
# Parameters of the SD models should be encapsulated in a named list
-Param2 <- list(`GaugingDown` = c(Velocity, Param))
+ParamGR4J <- c(X1 = 257.238, X2 = 1.012, X3 = 88.235, X4 = 2.208)
+Param <- list(`GaugingDown` = c(Velocity, ParamGR4J))
# RunModel for the whole network
OutputsModels <- RunModel(InputsModels,
- RunOptions = RunOptions2,
- Param = Param2)
+ RunOptions = RunOptions,
+ Param = Param)
str(OutputsModels)
-# Comparison between GRiwrm simulation and airGR simulation
-plot(OutputsModels, Qobs = data.frame(`GaugingDown` = OutputsModel$Qsim))
+# Compare Simulation with reservoir and observation of natural flow
+plot(OutputsModels, data.frame(GaugingDown = BasinObs$Qmm[Ind_Run]))
}
diff --git a/tests/testthat/helper_RunModel.R b/tests/testthat/helper_RunModel.R
index aeb7ec8..7c0913f 100644
--- a/tests/testthat/helper_RunModel.R
+++ b/tests/testthat/helper_RunModel.R
@@ -51,7 +51,7 @@ setupRunModel <- function() {
)
IndPeriod_WarmUp = seq(IndPeriod_Run[1]-365,IndPeriod_Run[1]-1)
RunOptions <- CreateRunOptions(
- InputsModel = InputsModel,
+ InputsModel,
IndPeriod_WarmUp = IndPeriod_WarmUp,
IndPeriod_Run = IndPeriod_Run
)
diff --git a/tests/testthat/helper_cemaneige.R b/tests/testthat/helper_cemaneige.R
index c62c66a..919312e 100644
--- a/tests/testthat/helper_cemaneige.R
+++ b/tests/testthat/helper_cemaneige.R
@@ -15,9 +15,7 @@
#' @examples
setUpCemaNeigeData <- function() {
- library(airGR)
data(L0123001)
- detach("package:airGR")
# Formatting observations for the hydrological models
# Each input data should be a matrix or a data.frame with the good id in the name of the column
diff --git a/tests/testthat/test-Calibration.R b/tests/testthat/test-Calibration.R
index a9e49ec..ecb3b98 100644
--- a/tests/testthat/test-Calibration.R
+++ b/tests/testthat/test-Calibration.R
@@ -1,12 +1,46 @@
+test_that("airGR::Calibration should work", {
+ ## loading catchment data
+ data(L0123001)
+
+ ## preparation of InputsModel object
+ InputsModel <- CreateInputsModel(RunModel_GR4J, DatesR = BasinObs$DatesR,
+ Precip = BasinObs$P, PotEvap = BasinObs$E)
+
+ ## calibration period selection
+ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1990-01-01"),
+ which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1999-12-31"))
+ Ind_WarmUp <- seq(which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1989-01-01"),
+ which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1989-12-31"))
+
+ ## preparation of RunOptions object
+ RunOptions <- CreateRunOptions(RunModel_GR4J,
+ InputsModel = InputsModel,
+ IndPeriod_Run = Ind_Run,
+ IndPeriod_WarmUp = Ind_WarmUp)
+
+ ## calibration criterion: preparation of the InputsCrit object
+ InputsCrit <- CreateInputsCrit(ErrorCrit_NSE, InputsModel = InputsModel,
+ RunOptions = RunOptions, Obs = BasinObs$Qmm[Ind_Run])
+
+ ## preparation of CalibOptions object
+ CalibOptions <- CreateCalibOptions(RunModel_GR4J, FUN_CALIB = Calibration_Michel)
+
+ ## calibration
+ OutputsCalib <- Calibration(InputsModel = InputsModel, RunOptions = RunOptions,
+ InputsCrit = InputsCrit, CalibOptions = CalibOptions,
+ FUN_MOD = RunModel_GR4J,
+ FUN_CALIB = Calibration_Michel)
+
+ expect_length(OutputsCalib$ParamFinalR, 4)
+})
+
# data set up
e <- setupRunModel()
# variables are copied from environment 'e' to the current environment
# https://stackoverflow.com/questions/9965577/r-copy-move-one-environment-to-another
for(x in ls(e)) assign(x, get(x, e))
-context("Calibration.GRiwrmInputsModel")
-
-CalibOptions <- CreateCalibOptions(InputsModel = InputsModel)
+CalibOptions <- CreateCalibOptions(InputsModel)
test_that("Calibrated parameters remains unchanged", {
InputsCrit <- CreateInputsCrit(
diff --git a/tests/testthat/test-CreateCalibOptions.R b/tests/testthat/test-CreateCalibOptions.R
new file mode 100644
index 0000000..4661409
--- /dev/null
+++ b/tests/testthat/test-CreateCalibOptions.R
@@ -0,0 +1,6 @@
+test_that("airGR::CreateCalibOptions should works", {
+ ## preparation of CalibOptions object
+ CalibOptions <- airGR::CreateCalibOptions(RunModel_GR4J, FUN_CALIB = Calibration_Michel)
+ expect_equal(CreateCalibOptions(RunModel_GR4J, FUN_CALIB = Calibration_Michel), CalibOptions)
+ expect_equal(CreateCalibOptions("RunModel_GR4J", FUN_CALIB = Calibration_Michel), CalibOptions)
+})
diff --git a/tests/testthat/test-CreateInputsCrit.R b/tests/testthat/test-CreateInputsCrit.R
index 99f00de..36b0eef 100644
--- a/tests/testthat/test-CreateInputsCrit.R
+++ b/tests/testthat/test-CreateInputsCrit.R
@@ -1,3 +1,34 @@
+test_that("airGR::CreateInputsCrit should works", {
+ ## loading catchment data
+ data(L0123001)
+
+ ## preparation of InputsModel object
+ InputsModel <- CreateInputsModel(RunModel_GR4J, DatesR = BasinObs$DatesR,
+ Precip = BasinObs$P, PotEvap = BasinObs$E)
+
+ ## calibration period selection
+ Ind_Run <- seq(which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1990-01-01"),
+ which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1999-12-31"))
+ Ind_WarmUp <- seq(which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1989-01-01"),
+ which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1989-12-31"))
+
+ ## preparation of RunOptions object
+ RunOptions <- CreateRunOptions(RunModel_GR4J,
+ InputsModel = InputsModel,
+ IndPeriod_Run = Ind_Run,
+ IndPeriod_WarmUp = Ind_WarmUp)
+
+ ## calibration criterion: preparation of the InputsCrit object
+ InputsCrit <- airGR::CreateInputsCrit(ErrorCrit_NSE, InputsModel = InputsModel,
+ RunOptions = RunOptions, Obs = BasinObs$Qmm[Ind_Run])
+ expect_equal(CreateInputsCrit(ErrorCrit_NSE, InputsModel = InputsModel,
+ RunOptions = RunOptions, Obs = BasinObs$Qmm[Ind_Run]),
+ InputsCrit)
+ expect_equal(CreateInputsCrit("ErrorCrit_NSE", InputsModel = InputsModel,
+ RunOptions = RunOptions, Obs = BasinObs$Qmm[Ind_Run]),
+ InputsCrit)
+})
+
# data set up
e <- setupRunModel()
# variables are copied from environment 'e' to the current environment
diff --git a/tests/testthat/test-CreateInputsModel.R b/tests/testthat/test-CreateInputsModel.R
index bc2d6d7..eb106bd 100644
--- a/tests/testthat/test-CreateInputsModel.R
+++ b/tests/testthat/test-CreateInputsModel.R
@@ -1,4 +1,23 @@
-context("CreateInputsModel")
+test_that("airGR::CreateInputsModel should work", {
+ ## loading catchment data
+ data(L0123001)
+
+ ## preparation of InputsModel object
+ InputsModel <- airGR::CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR,
+ Precip = BasinObs$P, PotEvap = BasinObs$E)
+
+ expect_equal(CreateInputsModel(RunModel_GR4J,
+ DatesR = BasinObs$DatesR,
+ Precip = BasinObs$P,
+ PotEvap = BasinObs$E),
+ InputsModel)
+ expect_equal(CreateInputsModel("RunModel_GR4J",
+ DatesR = BasinObs$DatesR,
+ Precip = BasinObs$P,
+ PotEvap = BasinObs$E),
+ InputsModel)
+})
+
l <- setUpCemaNeigeData()
diff --git a/tests/testthat/test-CreateRunOptions.R b/tests/testthat/test-CreateRunOptions.R
new file mode 100644
index 0000000..ed3e224
--- /dev/null
+++ b/tests/testthat/test-CreateRunOptions.R
@@ -0,0 +1,52 @@
+## loading catchment data
+data(L0123001)
+
+## preparation of InputsModel object
+InputsModel <- CreateInputsModel(RunModel_GR4J, DatesR = BasinObs$DatesR,
+ Precip = BasinObs$P, PotEvap = BasinObs$E)
+
+## calibration period selection
+Ind_Run <- seq(which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1990-01-01"),
+ which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1999-12-31"))
+Ind_WarmUp <- seq(which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1989-01-01"),
+ which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1989-12-31"))
+
+## preparation of RunOptions object
+RunOptions <- airGR::CreateRunOptions(RunModel_GR4J,
+ InputsModel = InputsModel,
+ IndPeriod_Run = Ind_Run,
+ IndPeriod_WarmUp = Ind_WarmUp)
+
+test_that("CreateRunOptions.InputsModel works", {
+ expect_equal(
+ CreateRunOptions(InputsModel,
+ FUN_MOD = RunModel_GR4J,
+ IndPeriod_Run = Ind_Run,
+ IndPeriod_WarmUp = Ind_WarmUp),
+ RunOptions)
+ InputsModel$FUN_MOD = RunModel_GR4J
+ expect_equal(
+ CreateRunOptions(InputsModel,
+ IndPeriod_Run = Ind_Run,
+ IndPeriod_WarmUp = Ind_WarmUp),
+ RunOptions)
+})
+
+test_that("CreateRunOptions.character works", {
+ expect_equal(
+ CreateRunOptions("RunModel_GR4J",
+ InputsModel = InputsModel,
+ IndPeriod_Run = Ind_Run,
+ IndPeriod_WarmUp = Ind_WarmUp),
+ RunOptions)
+})
+
+test_that("CreateRunOptions.function works", {
+ expect_equal(
+ CreateRunOptions(RunModel_GR4J,
+ InputsModel = InputsModel,
+ IndPeriod_Run = Ind_Run,
+ IndPeriod_WarmUp = Ind_WarmUp),
+ RunOptions)
+})
+
diff --git a/tests/testthat/test-RunModel.R b/tests/testthat/test-RunModel.R
index e20038a..f75b408 100644
--- a/tests/testthat/test-RunModel.R
+++ b/tests/testthat/test-RunModel.R
@@ -8,7 +8,7 @@ context("RunModel.GRiwrmInputsModel")
test_that("RunModel.GRiwrmInputsModel should return same result with separated warm-up", {
RO_WarmUp <- CreateRunOptions(
- InputsModel = InputsModel,
+ InputsModel,
IndPeriod_WarmUp = 0L,
IndPeriod_Run = IndPeriod_WarmUp
)
@@ -18,7 +18,7 @@ test_that("RunModel.GRiwrmInputsModel should return same result with separated w
Param = ParamMichel
)
RO_Run <- CreateRunOptions(
- InputsModel = InputsModel,
+ InputsModel,
IndPeriod_WarmUp = 0L,
IndPeriod_Run = IndPeriod_Run,
IniStates = lapply(OM_WarmUp, "[[", "StateEnd")
@@ -60,7 +60,9 @@ griwrm2 <- rbind(griwrm,
# Add Qobs for the 2 new nodes and create InputsModel
Qobs2 <- cbind(Qobs, matrix(data = rep(0, 2*nrow(Qobs)), ncol = 2))
colnames(Qobs2) <- c(colnames(Qobs2)[1:6], "R1", "R2")
-InputsModel <- CreateInputsModel(griwrm2, DatesR, Precip, PotEvap, Qobs2)
+InputsModel <- suppressWarnings(
+ CreateInputsModel(griwrm2, DatesR, Precip, PotEvap, Qobs2)
+)
test_that("RunModel.Supervisor with two regulations that cancel each other out should returns same results as RunModel.GRiwrmInputsModel", {
# Create Supervisor
@@ -103,14 +105,18 @@ test_that("RunModel.GRiwrmInputsModel handles CemaNeige", {
l$ZInputs <- l$ZInputs[1:2]
l$TempMean <- l$TempMean[,1:2]
l$HypsoData <- l$HypsoData[,1:2]
- InputsModels <- CreateInputsModel(l$griwrm,
- DatesR = l$DatesR,
- Precip = l$Precip,
- PotEvap = l$PotEvap,
- TempMean = l$TempMean,
- ZInputs = l$ZInputs,
- HypsoData = l$HypsoData,
- Qobs = l$Qobs)
+ InputsModels <- suppressWarnings(
+ CreateInputsModel(
+ l$griwrm,
+ DatesR = l$DatesR,
+ Precip = l$Precip,
+ PotEvap = l$PotEvap,
+ TempMean = l$TempMean,
+ ZInputs = l$ZInputs,
+ HypsoData = l$HypsoData,
+ Qobs = l$Qobs
+ )
+ )
## run period selection
Ind_Run <- seq(which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1990-01-01"),
which(format(BasinObs$DatesR, format = "%Y-%m-%d")=="1999-12-31"))
diff --git a/vignettes/V02_Calibration_SD_model.Rmd b/vignettes/V02_Calibration_SD_model.Rmd
index 074d7cd..19e4c96 100644
--- a/vignettes/V02_Calibration_SD_model.Rmd
+++ b/vignettes/V02_Calibration_SD_model.Rmd
@@ -74,7 +74,7 @@ Arguments of the `CreateRunOptions` function for **airGRiwrm** are the same as f
```{r}
RunOptions <- CreateRunOptions(
- InputsModel = InputsModel,
+ InputsModel,
IndPeriod_WarmUp = IndPeriod_WarmUp,
IndPeriod_Run = IndPeriod_Run
)
@@ -98,7 +98,7 @@ It needs the following arguments:
```{r InputsCrit}
InputsCrit <- CreateInputsCrit(
InputsModel = InputsModel,
- FUN_CRIT = airGR::ErrorCrit_KGE2,
+ FUN_CRIT = ErrorCrit_KGE2,
RunOptions = RunOptions,
Obs = Qobs[IndPeriod_Run, ],
AprioriIds = c(
diff --git a/vignettes/V03_Open-loop_influenced_flow.Rmd b/vignettes/V03_Open-loop_influenced_flow.Rmd
index 2895ee9..35bb05f 100644
--- a/vignettes/V03_Open-loop_influenced_flow.Rmd
+++ b/vignettes/V03_Open-loop_influenced_flow.Rmd
@@ -103,7 +103,7 @@ RunOptions <- CreateRunOptions(IM_OL,
IndPeriod_WarmUp = IndPeriod_WarmUp,
IndPeriod_Run = IndPeriod_Run)
InputsCrit <- CreateInputsCrit(IM_OL,
- FUN_CRIT = airGR::ErrorCrit_KGE2,
+ FUN_CRIT = ErrorCrit_KGE2,
RunOptions = RunOptions, Obs = Qobs[IndPeriod_Run,],
AprioriIds = c("54057" = "54032", "54032" = "54001"),
transfo = "sqrt", k = 0.15
diff --git a/vignettes/V04_Closed-loop_regulated_withdrawal.Rmd b/vignettes/V04_Closed-loop_regulated_withdrawal.Rmd
index dd39ea6..50a606b 100644
--- a/vignettes/V04_Closed-loop_regulated_withdrawal.Rmd
+++ b/vignettes/V04_Closed-loop_regulated_withdrawal.Rmd
@@ -87,7 +87,7 @@ PotEvap <- ConvertMeteoSD(griwrm, PotEvapTot)
# Calculation of the water need at the sub-basin scale
dailyWaterNeed <- PotEvap - Precip
dailyWaterNeed <- cbind(as.data.frame(DatesR), dailyWaterNeed[,c("54001", "54032")])
-monthlyWaterNeed <- airGR::SeriesAggreg(dailyWaterNeed, "%m", rep("q80",2))
+monthlyWaterNeed <- SeriesAggreg(dailyWaterNeed, "%m", rep("q80",2))
monthlyWaterNeed$DatesR <- as.numeric(format(monthlyWaterNeed$DatesR,"%m"))
names(monthlyWaterNeed)[1] <- "month"
monthlyWaterNeed
diff --git a/vignettes/seinebasin/V02_First_run.Rmd b/vignettes/seinebasin/V02_First_run.Rmd
index 151b953..19d5976 100644
--- a/vignettes/seinebasin/V02_First_run.Rmd
+++ b/vignettes/seinebasin/V02_First_run.Rmd
@@ -95,7 +95,7 @@ IndPeriod_WarmUp <- seq(1, IndPeriod_Run[1] - 1)
```{r CreateRunOptions}
RunOptions <- CreateRunOptions(
- InputsModel = InputsModel,
+ InputsModel,
IndPeriod_WarmUp = IndPeriod_WarmUp,
IndPeriod_Run = IndPeriod_Run
)
diff --git a/vignettes/seinebasin/V03_First_Calibration.Rmd b/vignettes/seinebasin/V03_First_Calibration.Rmd
index b98734e..438e2ae 100644
--- a/vignettes/seinebasin/V03_First_Calibration.Rmd
+++ b/vignettes/seinebasin/V03_First_Calibration.Rmd
@@ -32,7 +32,7 @@ We need then to prepare the InputsCrit object that is necessary to define the ca
```{r CreateInputsCrit}
InputsCrit <- CreateInputsCrit(
InputsModel = InputsModel,
- FUN_CRIT = airGR::ErrorCrit_KGE2,
+ FUN_CRIT = ErrorCrit_KGE2,
RunOptions = RunOptions,
Obs = Qnat[IndPeriod_Run,]
)
diff --git a/vignettes/seinebasin/V04_Open-loop_influenced_flow.Rmd b/vignettes/seinebasin/V04_Open-loop_influenced_flow.Rmd
index b95efee..3e800de 100644
--- a/vignettes/seinebasin/V04_Open-loop_influenced_flow.Rmd
+++ b/vignettes/seinebasin/V04_Open-loop_influenced_flow.Rmd
@@ -249,7 +249,7 @@ We can now run the model, using the parameters previously obtained:
```{r RunModel}
RunOptions <- CreateRunOptions(
- InputsModel = InputsModel2,
+ InputsModel2,
IndPeriod_Run = IndPeriod_Run
)
OutputsModels2 <- RunModel(
diff --git a/vignettes/seinebasin/V05_Open-loop_influenced_flow_calibration.Rmd b/vignettes/seinebasin/V05_Open-loop_influenced_flow_calibration.Rmd
index 164f551..3005233 100644
--- a/vignettes/seinebasin/V05_Open-loop_influenced_flow_calibration.Rmd
+++ b/vignettes/seinebasin/V05_Open-loop_influenced_flow_calibration.Rmd
@@ -75,7 +75,7 @@ IndPeriod_WarmUp <- seq.int(1, IndPeriod_Run[1] - 1)
```{r CreateRunOptions}
RunOptions <- CreateRunOptions(
- InputsModel = InputsModel3,
+ InputsModel3,
IndPeriod_WarmUp = IndPeriod_WarmUp,
IndPeriod_Run = IndPeriod_Run
)
@@ -88,7 +88,7 @@ We define the objective function for the calibration:
```{r CreateInputsCrit}
InputsCrit <- CreateInputsCrit(
InputsModel = InputsModel3,
- FUN_CRIT = airGR::ErrorCrit_KGE2,
+ FUN_CRIT = ErrorCrit_KGE2,
RunOptions = RunOptions, Obs = Qobs[IndPeriod_Run,]
)
```
diff --git a/vignettes/seinebasin/V05b_Open-loop_influenced_flow_calibration_GR6J.Rmd b/vignettes/seinebasin/V05b_Open-loop_influenced_flow_calibration_GR6J.Rmd
index b132e5a..f5aa8fb 100644
--- a/vignettes/seinebasin/V05b_Open-loop_influenced_flow_calibration_GR6J.Rmd
+++ b/vignettes/seinebasin/V05b_Open-loop_influenced_flow_calibration_GR6J.Rmd
@@ -77,7 +77,7 @@ IndPeriod_WarmUp <- seq.int(1,IndPeriod_Run[1] - 1)
```{r CreateRunOptions}
RunOptions <- CreateRunOptions(
- InputsModel = InputsModel3,
+ InputsModel3,
IndPeriod_WarmUp = IndPeriod_WarmUp,
IndPeriod_Run = IndPeriod_Run
)
@@ -90,7 +90,7 @@ We define the objective function for the calibration:
```{r CreateInputsCrit}
InputsCrit <- CreateInputsCrit(
InputsModel = InputsModel3,
- FUN_CRIT = airGR::ErrorCrit_KGE2,
+ FUN_CRIT = ErrorCrit_KGE2,
RunOptions = RunOptions, Obs = Qobs[IndPeriod_Run,]
)
```
diff --git a/vignettes/seinebasin/V06_Naturalised_flow_simulation.Rmd b/vignettes/seinebasin/V06_Naturalised_flow_simulation.Rmd
index 20a52b5..4b0a8f2 100644
--- a/vignettes/seinebasin/V06_Naturalised_flow_simulation.Rmd
+++ b/vignettes/seinebasin/V06_Naturalised_flow_simulation.Rmd
@@ -77,7 +77,7 @@ IndPeriod_WarmUp <- seq(1, IndPeriod_Run[1] - 1)
```{r CreateRunOptions}
RunOptions <- CreateRunOptions(
- InputsModel = InputsModel4,
+ InputsModel4,
IndPeriod_WarmUp = IndPeriod_WarmUp,
IndPeriod_Run = IndPeriod_Run
)
--
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