From 0ed4b8761b551d979abfa50c5f565ab330052bac Mon Sep 17 00:00:00 2001
From: Dorchies David <david.dorchies@irstea.fr>
Date: Tue, 26 May 2020 17:34:38 +0200
Subject: [PATCH] feat: Overriding airGR CreateInputsModel, RunOptions and
RunModel
Fix #4
---
NAMESPACE | 14 ++-
R/CreateInputsModel.Griwrm.R | 95 +++++++++++++++++++
R/CreateInputsModel.R | 123 -------------------------
R/CreateInputsModel.default.R | 35 +++++++
R/CreateRunOptions.GriwrmInputsModel.R | 44 +++++++++
R/CreateRunOptions.InputsModel.R | 40 ++++++++
R/CreateRunOptions.R | 12 +++
R/RunModel.GriwrmInputsModel.R | 46 +++++++++
R/RunModel.InputsModel.R | 17 ++++
R/RunModel.R | 12 +++
R/RunModelGriwrm.R | 107 ---------------------
vignettes/01_First_network.Rmd | 7 +-
vignettes/02_First_run.Rmd | 62 +++++++++++--
13 files changed, 368 insertions(+), 246 deletions(-)
create mode 100644 R/CreateInputsModel.Griwrm.R
create mode 100644 R/CreateInputsModel.default.R
create mode 100644 R/CreateRunOptions.GriwrmInputsModel.R
create mode 100644 R/CreateRunOptions.InputsModel.R
create mode 100644 R/CreateRunOptions.R
create mode 100644 R/RunModel.GriwrmInputsModel.R
create mode 100644 R/RunModel.InputsModel.R
create mode 100644 R/RunModel.R
delete mode 100644 R/RunModelGriwrm.R
diff --git a/NAMESPACE b/NAMESPACE
index 65e3699..4a6bcd8 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,10 +1,20 @@
# Generated by roxygen2: do not edit by hand
+S3method(Calibration,default)
+S3method(Calibration,griwrm)
+S3method(CreateInputsModel,Griwrm)
+S3method(CreateInputsModel,default)
+S3method(CreateRunOptions,GriwrmInputsModel)
+S3method(CreateRunOptions,InputsModel)
+S3method(RunModel,GriwrmInputsModel)
+S3method(RunModel,InputsModel)
S3method(merge,Gits)
+export(Calibration)
+export(CreateInputsModel)
+export(CreateRunOptions)
export(Ginet)
export(Girop)
export(Gits)
-export(RunModelGriwrm)
-export(SetAirGrInputsAndOptions)
+export(RunModel)
export(getNodeRanking)
import(airGR)
diff --git a/R/CreateInputsModel.Griwrm.R b/R/CreateInputsModel.Griwrm.R
new file mode 100644
index 0000000..9dc04d8
--- /dev/null
+++ b/R/CreateInputsModel.Griwrm.R
@@ -0,0 +1,95 @@
+#' Create InputsModel object for a GRIWRM network
+#'
+#' @param ginet
+#' @param girop
+#' @param gits
+#'
+#' @return
+#' @export
+#'
+#' @examples
+CreateInputsModel.Griwrm <- function(ginet, girop, gits, verbose = TRUE) {
+
+ InputsModel <- CreateEmptyGriwrmInputsModel()
+
+ for(id in getNodeRanking(ginet)) {
+ if(verbose) cat("CreateInputsModel.griwrm: Treating sub-basin", id, "...\n")
+ InputsModel[[id]] <- CreateOneGriwrmInputsModel(id, ginet, girop, gits)
+ }
+ return(InputsModel)
+}
+
+
+#' Create an empty InputsModel object for GRIWRM nodes
+#'
+#' @return
+#'
+#' @examples
+CreateEmptyGriwrmInputsModel <- function() {
+ InputsModel <- list()
+ class(InputsModel) <- append(class(InputsModel), "GriwrmInputsModel")
+ return(InputsModel)
+}
+
+
+#' Create one InputsModel for a GRIWRM node
+#'
+#' @param ginet
+#' @param girop
+#' @param gits
+#' @param id
+#'
+#' @return
+#'
+#' @examples
+CreateOneGriwrmInputsModel <- function(id, ginet, girop, gits) {
+ node <- ginet[ginet$id == id,]
+ FUN_MOD <- girop$model[girop$id == id]
+
+ # Set hydraulic parameters
+ UpstreamNodes <- ginet$id[ginet$down == id & !is.na(ginet$down)]
+ QobsUpstr <- NULL
+ LengthHydro <- NULL
+ BasinAreas <- NULL
+
+ if(length(UpstreamNodes) > 0) {
+ # Sub-basin with hydraulic routing
+ for(idUpstrNode in UpstreamNodes) {
+ QobsUpstr1 <- matrix(gits[[idUpstrNode]]$Qobs, ncol = 1)
+ if(is.null(QobsUpstr)) {
+ QobsUpstr <- QobsUpstr1
+ } else {
+ QobsUpstr <- cbind(QobsUpstr, QobsUpstr1)
+ }
+ }
+ LengthHydro <- matrix(ginet$length[girop$id %in% UpstreamNodes] , nrow = 1)
+ BasinAreas <- matrix(
+ c(
+ girop$area[girop$id %in% UpstreamNodes],
+ girop$area[girop$id == id] - sum(girop$area[girop$id %in% UpstreamNodes])
+ ),
+ nrow = 1
+ )
+ }
+
+ # Set model inputs with the airGR function
+ InputsModel <- CreateInputsModel(
+ FUN_MOD,
+ DatesR = gits$date,
+ Precip = gits[[id]]$Precip,
+ PotEvap = gits[[id]]$PotEvap,
+ QobsUpstr = QobsUpstr,
+ LengthHydro = LengthHydro,
+ BasinAreas = BasinAreas
+ )
+
+ # Add Identifiers of connected nodes in order to be able to update them with simulated flows
+ InputsModel$id <- id
+ if(length(UpstreamNodes) > 0) {
+ InputsModel$UpstreamNodes <- UpstreamNodes
+ }
+ # Add the model function
+ InputsModel$FUN_MOD <- FUN_MOD
+
+ return(InputsModel)
+}
diff --git a/R/CreateInputsModel.R b/R/CreateInputsModel.R
index 72eb3fa..af0e772 100644
--- a/R/CreateInputsModel.R
+++ b/R/CreateInputsModel.R
@@ -10,126 +10,3 @@
CreateInputsModel <- function(x, ...) {
UseMethod("CreateInputsModel", x)
}
-
-#' Wrapper for the airGR::CreateInputsModel function
-#'
-#' @param FUN_MOD
-#' @param DatesR
-#' @param Precip
-#' @param PrecipScale
-#' @param PotEvap
-#' @param TempMean
-#' @param TempMin
-#' @param TempMax
-#' @param ZInputs
-#' @param HypsoData
-#' @param NLayers
-#' @param QobsUpstr
-#' @param LengthHydro
-#' @param BasinAreas
-#' @param verbose
-#'
-#' @return
-#' @export
-#'
-#' @examples
-CreateInputsModel.default <- function(FUN_MOD,
- DatesR,
- Precip, PrecipScale = TRUE,
- PotEvap = NULL,
- TempMean = NULL, TempMin = NULL, TempMax = NULL,
- ZInputs = NULL, HypsoData = NULL, NLayers = 5,
- QobsUpstr = NULL, LengthHydro = NULL, BasinAreas = NULL,
- verbose = TRUE) {
- airGR::CreateInputsModel(FUN_MOD, DatesR, Precip, PrecipScale, PotEvap,
- TempMean, TempMin, TempMax, ZInputs, HypsoData, NLayers,
- QobsUpstr, LengthHydro, BasinAreas, verbose)
-}
-
-
-#' Create InputsModel object for a GRIWRM network
-#'
-#' @param ginet
-#' @param girop
-#' @param gits
-#'
-#' @return
-#' @export
-#'
-#' @examples
-CreateInputsModel.Griwrm <- function(ginet, girop, gits, verbose = TRUE) {
-
- InputsModel <- CreateEmptyGriwrmInputsModel()
-
- for(id in getNodeRanking(ginet)) {
- if(verbose) cat("CreateInputsModel.griwrm: Treating sub-basin", id, "...\n")
- InputsModel[[id]] <- CreateOneGriwrmInputsModel(id, ginet, girop, gits)
- }
-}
-
-
-#' Create an empty InputsModel object for GRIWRM
-#'
-#' @return
-#' @export
-#'
-#' @examples
-CreateEmptyGriwrmInputsModel <- function() {
- InputsModel <- list()
- class(InputsModel) <- append(class(InputsModel), "GriwrmInputsModel")
- return(InputsModel)
-}
-
-
-#' Create one InputsModel for a GRIWRM node
-#'
-#' @param ginet
-#' @param girop
-#' @param gits
-#' @param id
-#'
-#' @return
-#' @export
-#'
-#' @examples
-CreateOneGriwrmInputsModel <- function(id, ginet, girop, gits) {
- node <- ginet[ginet$id == id,]
- FUN_MOD <- girop$model[girop$id == id]
-
- # Set hydraulic parameters
- UpstrNodes <- ginet$id[ginet$down == id & !is.na(ginet$down)]
- QobsUpstr <- NULL
- LengthHydro <- NULL
- BasinAreas <- NULL
-
- if(length(UpstrNodes) > 0) {
- # Sub-basin with hydraulic routing
- for(idUpstrNode in UpstrNodes) {
- QobsUpstr1 <- matrix(gits[[idUpstrNode]]$Qobs, ncol = 1)
- if(is.null(QobsUpstr)) {
- QobsUpstr <- QobsUpstr1
- } else {
- QobsUpstr <- cbind(QobsUpstr, QobsUpstr1)
- }
- }
- LengthHydro <- matrix(ginet$length[girop$id %in% UpstrNodes] , nrow = 1)
- BasinAreas <- matrix(
- c(
- girop$area[girop$id %in% UpstrNodes],
- girop$area[girop$id == id] - sum(girop$area[girop$id %in% UpstrNodes])
- ),
- nrow = 1
- )
- }
-
- # Set model inputs
- CreateInputsModel(
- FUN_MOD,
- DatesR = gits$date,
- Precip = gits[[id]]$Precip,
- PotEvap = gits[[id]]$PotEvap,
- QobsUpstr = QobsUpstr,
- LengthHydro = LengthHydro,
- BasinAreas = BasinAreas
- )
-}
diff --git a/R/CreateInputsModel.default.R b/R/CreateInputsModel.default.R
new file mode 100644
index 0000000..6af6189
--- /dev/null
+++ b/R/CreateInputsModel.default.R
@@ -0,0 +1,35 @@
+#' Wrapper for the airGR::CreateInputsModel function
+#'
+#' @param FUN_MOD
+#' @param DatesR
+#' @param Precip
+#' @param PrecipScale
+#' @param PotEvap
+#' @param TempMean
+#' @param TempMin
+#' @param TempMax
+#' @param ZInputs
+#' @param HypsoData
+#' @param NLayers
+#' @param QobsUpstr
+#' @param LengthHydro
+#' @param BasinAreas
+#' @param verbose
+#'
+#' @return
+#' @import airGR
+#' @export
+#'
+#' @examples
+CreateInputsModel.default <- function(FUN_MOD,
+ DatesR,
+ Precip, PrecipScale = TRUE,
+ PotEvap = NULL,
+ TempMean = NULL, TempMin = NULL, TempMax = NULL,
+ ZInputs = NULL, HypsoData = NULL, NLayers = 5,
+ QobsUpstr = NULL, LengthHydro = NULL, BasinAreas = NULL,
+ verbose = TRUE) {
+ airGR::CreateInputsModel(FUN_MOD, DatesR, Precip, PrecipScale, PotEvap,
+ TempMean, TempMin, TempMax, ZInputs, HypsoData, NLayers,
+ QobsUpstr, LengthHydro, BasinAreas, verbose)
+}
diff --git a/R/CreateRunOptions.GriwrmInputsModel.R b/R/CreateRunOptions.GriwrmInputsModel.R
new file mode 100644
index 0000000..a67b084
--- /dev/null
+++ b/R/CreateRunOptions.GriwrmInputsModel.R
@@ -0,0 +1,44 @@
+#' Title
+#'
+#' @param InputsModel
+#' @param IndPeriod_WarmUp
+#' @param IndPeriod_Run
+#' @param IniStates
+#' @param IniResLevels
+#' @param Imax
+#' @param Outputs_Cal
+#' @param Outputs_Sim
+#' @param MeanAnSolidPrecip
+#' @param IsHyst
+#' @param warnings
+#' @param verbose
+#'
+#' @return
+#' @export
+#'
+#' @examples
+CreateRunOptions.GriwrmInputsModel <- function(InputsModel, IndPeriod_WarmUp = NULL, IndPeriod_Run,
+ IniStates = NULL, IniResLevels = NULL, Imax = NULL,
+ Outputs_Cal = NULL, Outputs_Sim = "all",
+ MeanAnSolidPrecip = NULL, IsHyst = FALSE,
+ warnings = TRUE, verbose = TRUE) {
+ RunOptions <- list()
+ class(RunOptions) <- append(class(RunOptions), "GriwrmRunOptions")
+ for(InputsModelBasin in InputsModel) {
+ RunOptions[[InputsModelBasin$id]] <- CreateRunOptions(
+ InputsModel = InputsModelBasin,
+ IndPeriod_WarmUp = IndPeriod_WarmUp,
+ IndPeriod_Run = IndPeriod_Run,
+ IniStates = IniStates,
+ IniResLevels = IniResLevels,
+ Imax = Imax,
+ Outputs_Cal = Outputs_Cal,
+ Outputs_Sim = Outputs_Sim,
+ MeanAnSolidPrecip = MeanAnSolidPrecip,
+ IsHyst = IsHyst,
+ warnings = warnings,
+ verbose = verbose
+ )
+ }
+ return(RunOptions)
+}
diff --git a/R/CreateRunOptions.InputsModel.R b/R/CreateRunOptions.InputsModel.R
new file mode 100644
index 0000000..f451e68
--- /dev/null
+++ b/R/CreateRunOptions.InputsModel.R
@@ -0,0 +1,40 @@
+#' Title
+#'
+#' @param FUN_MOD
+#' @param InputsModel
+#' @param IndPeriod_WarmUp
+#' @param IndPeriod_Run
+#' @param IniStates
+#' @param IniResLevels
+#' @param Imax
+#' @param Outputs_Cal
+#' @param Outputs_Sim
+#' @param MeanAnSolidPrecip
+#' @param IsHyst
+#' @param warnings
+#' @param verbose
+#'
+#' @return
+#' @export
+#'
+#' @examples
+CreateRunOptions.InputsModel <- function(InputsModel,
+ IndPeriod_WarmUp = NULL, IndPeriod_Run,
+ IniStates = NULL, IniResLevels = NULL, Imax = NULL,
+ Outputs_Cal = NULL, Outputs_Sim = "all",
+ MeanAnSolidPrecip = NULL, IsHyst = FALSE,
+ warnings = TRUE, verbose = TRUE) {
+ airGR::CreateRunOptions(FUN_MOD = InputsModel$FUN_MOD,
+ InputsModel = InputsModel,
+ IndPeriod_WarmUp = IndPeriod_WarmUp,
+ IndPeriod_Run = IndPeriod_Run,
+ IniStates = IniStates,
+ IniResLevels = IniResLevels,
+ Imax = Imax,
+ Outputs_Cal = Outputs_Cal,
+ Outputs_Sim = Outputs_Sim,
+ MeanAnSolidPrecip = MeanAnSolidPrecip,
+ IsHyst = IsHyst,
+ warnings = warnings,
+ verbose = verbose)
+}
diff --git a/R/CreateRunOptions.R b/R/CreateRunOptions.R
new file mode 100644
index 0000000..55b0a80
--- /dev/null
+++ b/R/CreateRunOptions.R
@@ -0,0 +1,12 @@
+#' Title
+#'
+#' @param ...
+#' @param InputsModel
+#'
+#' @return
+#' @export
+#'
+#' @examples
+CreateRunOptions <- function(InputsModel, ...) {
+ UseMethod("CreateRunOptions", InputsModel)
+}
diff --git a/R/RunModel.GriwrmInputsModel.R b/R/RunModel.GriwrmInputsModel.R
new file mode 100644
index 0000000..87e2210
--- /dev/null
+++ b/R/RunModel.GriwrmInputsModel.R
@@ -0,0 +1,46 @@
+#' Title
+#'
+#' @param ginet
+#' @param girop
+#' @param gits
+#' @param IndPeriod_Run
+#' @param IndPeriod_WarmUp
+#'
+#' @return
+#' @export
+#'
+#' @examples
+RunModel.GriwrmInputsModel <- function(InputsModel, RunOptions, girop, verbose = TRUE) {
+
+ OutputsModels <- list()
+
+ for(IM in InputsModel) {
+ if(verbose) cat("RunModel.GriwrmInputsModel: Treating sub-basin", IM$id, "...\n")
+
+ # Update InputsModel$QobsUpstr with simulated upstream flows
+ if(length(IM$UpstreamNodes) > 0) {
+ for(i in 1:length(IM$UpstreamNodes)) {
+ QobsUpstr1 <- matrix(
+ c(
+ rep(0, length(RunOptions[[IM$id]]$IndPeriod_WarmUp)),
+ OutputsModels[[IM$UpstreamNodes[i]]]$Qsim
+ ), ncol = 1
+ )
+ if(i == 1) {
+ IM$QobsUpstr <- QobsUpstr1
+ } else {
+ IM$QobsUpstr <- cbind(IM$QobsUpstr, QobsUpstr1)
+ }
+ }
+ }
+
+ # Run the model for the sub-basin
+ OutputsModels[[IM$id]] <- RunModel(
+ InputsModel = IM,
+ RunOptions = RunOptions[[IM$id]],
+ Param = unlist(girop$params[girop$id == IM$id])
+ )
+
+ }
+ return(OutputsModels)
+}
diff --git a/R/RunModel.InputsModel.R b/R/RunModel.InputsModel.R
new file mode 100644
index 0000000..5aef686
--- /dev/null
+++ b/R/RunModel.InputsModel.R
@@ -0,0 +1,17 @@
+#' Wrapper for \code{\link[airGR]{RunModel}} which performs a single model run with the provided function over the selected period.
+#'
+#' @param InputsModel object of class \emph{InputsModel}, see \code{\link[airGR]{CreateInputsModel}} for details.
+#' @param RunOptions object of class \emph{RunOptions}, see \code{\link[airGR]{CreateRunOptions}} for details.
+#' @param Param numeric vector of model parameters.
+#' @param FUN_MOD hydrological model function (e.g. \code{\link[airGR]{RunModel_GR4J}}, \code{\link[airGR]{RunModel_CemaNeigeGR4J}}).
+#'
+#' @return
+#' @export
+#'
+#' @examples
+RunModel.InputsModel <- function(InputsModel, RunOptions, Param, FUN_MOD = NULL) {
+ if(is.null(FUN_MOD)) {
+ FUN_MOD <- InputsModel$FUN_MOD
+ }
+ airGR::RunModel(InputsModel, RunOptions, Param, FUN_MOD)
+}
diff --git a/R/RunModel.R b/R/RunModel.R
new file mode 100644
index 0000000..89b202e
--- /dev/null
+++ b/R/RunModel.R
@@ -0,0 +1,12 @@
+#' RunModel function for both airGR and GriwrmInputsModel object
+#'
+#' @param InputsModel
+#' @param ...
+#'
+#' @return
+#' @export
+#'
+#' @examples
+RunModel <- function(InputsModel, ...) {
+ UseMethod("RunModel", InputsModel)
+}
diff --git a/R/RunModelGriwrm.R b/R/RunModelGriwrm.R
deleted file mode 100644
index 2cc7687..0000000
--- a/R/RunModelGriwrm.R
+++ /dev/null
@@ -1,107 +0,0 @@
-#' Title
-#'
-#' @param ginet
-#' @param girop
-#' @param gits
-#' @param IndPeriod_Run
-#' @param IndPeriod_WarmUp
-#'
-#' @return
-#' @import airGR
-#' @export
-#'
-#' @examples
-RunModelGriwrm <- function(ginet, girop, gits, IndPeriod_Run, IndPeriod_WarmUp = NULL, verbose = TRUE) {
-
- OutputsModels <- list()
-
- for(id in getNodeRanking(ginet)) {
- if(verbose) cat("*** Treating sub-basin", id, "... ***\n")
-
- # Set InputsModel and RunOptions
- lIO <- SetAirGrInputsAndOptions(
- id, ginet, girop, gits, OutputsModels,
- IndPeriod_Run, IndPeriod_WarmUp
- )
-
- # Prepare param for upstream sub-basin or basin with hydraulic routing
- Param <- unlist(girop$params[girop$id == id])
-
- # Run the model for the sub-basin
- OutputsModels[[id]] <- RunModel(
- FUN_MOD = girop$model[girop$id == id],
- InputsModel = lIO$InputsModel,
- RunOptions = lIO$RunOptions,
- Param = Param
- )
-
- }
- OutputsModels
-}
-
-#' Title
-#'
-#' @param id
-#' @param ginet
-#' @param girop
-#' @param gits
-#' @param IndPeriod_Run
-#' @param IndPeriod_WarmUp
-#'
-#' @return
-#' @import airGR
-#' @export
-#'
-#' @examples
-SetAirGrInputsAndOptions <- function(id, ginet, girop, gits, OutputsModels, IndPeriod_Run, IndPeriod_WarmUp = NULL) {
- node <- ginet[ginet$id == id,]
- FUN_MOD <- girop$model[girop$id == id]
- # Set hydraulic parameters
- UpstrNodes <- ginet$id[ginet$down == id & !is.na(ginet$down)]
- if(length(UpstrNodes) == 0) {
- # Upstream sub-basin
- QobsUpstr <- NULL
- LengthHydro <- NULL
- BasinAreas <- NULL
- } else {
- # Sub-basin with hydraulic routing
- for(i in 1:length(UpstrNodes)) {
- QobsUpstr1 <- matrix(
- c(
- rep(0, length(IndPeriod_WarmUp)),
- OutputsModels[[UpstrNodes[i]]]$Qsim
- ), ncol = 1
- )
- if(i == 1) {
- QobsUpstr <- QobsUpstr1
- } else {
- QobsUpstr <- cbind(QobsUpstr, QobsUpstr1)
- }
- }
- LengthHydro <- matrix(ginet$length[girop$id %in% UpstrNodes] , nrow = 1)
- BasinAreas <- matrix(
- c(
- girop$area[girop$id %in% UpstrNodes],
- girop$area[girop$id == id] - sum(girop$area[girop$id %in% UpstrNodes])
- ),
- nrow = 1
- )
- }
- # Set model inputs
- InputsModel <- CreateInputsModel(
- FUN_MOD = FUN_MOD,
- DatesR = gits$date,
- Precip = gits[[id]]$Precip,
- PotEvap = gits[[id]]$PotEvap,
- QobsUpstr = QobsUpstr,
- LengthHydro = LengthHydro,
- BasinAreas = BasinAreas
- )
- # Set model options
- RunOptions <- CreateRunOptions(
- FUN_MOD = FUN_MOD,
- InputsModel = InputsModel, IndPeriod_Run = IndPeriod_Run,
- IniStates = NULL, IniResLevels = NULL, IndPeriod_WarmUp = IndPeriod_WarmUp
- )
- list(InputsModel = InputsModel, RunOptions = RunOptions)
-}
diff --git a/vignettes/01_First_network.Rmd b/vignettes/01_First_network.Rmd
index 1c935c7..8e7974f 100644
--- a/vignettes/01_First_network.Rmd
+++ b/vignettes/01_First_network.Rmd
@@ -80,10 +80,9 @@ load_ts <- function(x) {
delim = ";", skip = 16, trim_ws = TRUE)
ts$Date <- as.POSIXlt(lubridate::ymd(ts$Date))
# Interpolation of data gap in the discharge time serie
- browser
ts[ts$Qnat < 0, "Qnat"] <- NA
if(is.na(ts$Qnat[nrow(ts)])) {
- ts$Qnat[nrow(ts)] <- 0 # End of time series converge to zero
+ ts$Qnat[nrow(ts)] <- 0 # No value at the end: time serie converge to zero
}
ts$Qnat <- zoo::na.approx(ts$Qnat)
ts
@@ -120,7 +119,7 @@ The airGR CreateInputsModel function is extended in order to handle the ginet ob
```{r}
- InputsModel <- CreateInputsModel(ginet, girop, gits)
+InputsModel <- CreateInputsModel(ginet, girop, gits)
```
@@ -129,6 +128,6 @@ The airGR CreateInputsModel function is extended in order to handle the ginet ob
```{r}
dir.create("_cache", showWarnings = FALSE)
-save(ginet, girop, gits, file = "_cache/seine.RData")
+save(ginet, girop, gits, InputsModel, file = "_cache/seine.RData")
```
diff --git a/vignettes/02_First_run.Rmd b/vignettes/02_First_run.Rmd
index bc8ba93..e965f29 100644
--- a/vignettes/02_First_run.Rmd
+++ b/vignettes/02_First_run.Rmd
@@ -9,13 +9,25 @@ output: html_document
knitr::opts_chunk$set(echo = TRUE)
```
-## Load parameters of GR4 run-off model
+## Load libraries
```{r}
library(griwrm)
+```
+
+
+## Load parameters of GR4 run-off model
+
+### Loading network and time series data
+
+Run `vignette("01_First_network", package = "griwrm")` before this one in order to create the Rdata file loaded below:
+
+```{r}
load("_cache/seine.RData")
```
+### Loading
+
Data comes from calibration of ClimAware project with naturalised flows.
```{r}
@@ -27,7 +39,7 @@ ClimAwareParams
```
The lag $\tau_0$ and route $K_0$ parameters of TGR are expressed as time delay in hours corresponding to the delay time between the farest upstream inlet and the outlet of the sub-basin.
-Almost all sub basin has only a lag parameter. The only exception is for La Marne àNoisiel (NOISI_17) that has a routing parameter which can be approximated to a single lag parameter equals to $\tau_0 + K_0$.
+Almost all sub basin has only a lag parameter. The only exception is for La Marne à Noisiel (NOISI_17) that has a routing parameter which can be approximated to a single lag parameter equals to $\tau_0 + K_0$.
This lag parameter has to be converted in a speed in m/s used in the airGR lag model:
@@ -48,22 +60,52 @@ for(id in girop$id) {
girop$params[girop$id == id] <- list(params[params$id == id, c("S", "IGF", "KR", "T", sLag)])
}
+dplyr::select(params, id, S, IGF, KR, T, LAG)
```
-## Run the SD model for the whole basin
+## GriwmRunOptions object
+
+The `CreateRunOptions()` function allows to prepare the options required to the `RunModel()` function.
+
+The user must at least define the following arguments:
+
+* InputsModel: the associated input data
+* IndPeriod_Run: the period on which the model is run
+
```{r}
-# Time settings
library(lubridate)
IndPeriod_Run <- seq(
- which(gits$date == (gits$date[1] + months(12))), # Set aside warm-up period
- length(gits$date)) # Until the end of the time series
+ which(InputsModel[[1]]$DatesR == (InputsModel[[1]]$DatesR[1] + months(12))), # Set aside warm-up period
+ length(InputsModel[[1]]$DatesR) # Until the end of the time series
+)
+```
+
+The warmup period could also be defined as is:
+
+```{r}
IndPeriod_WarmUp = seq(1,IndPeriod_Run[1]-1)
+```
-OutputsModels <- RunModelGriwrm(
- ginet, girop, gits,
- IndPeriod_Run = IndPeriod_Run,
- IndPeriod_WarmUp = IndPeriod_WarmUp
+
+
+```{r}
+RunOptions <- CreateRunOptions(
+ InputsModel = InputsModel,
+ IndPeriod_WarmUp = IndPeriod_WarmUp,
+ IndPeriod_Run = IndPeriod_Run
+)
+```
+
+
+
+## Run the SD model for the whole basin
+
+```{r}
+OutputsModels <- RunModel(
+ InputsModel = InputsModel,
+ RunOptions = RunOptions,
+ girop
)
```
--
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