doc(vignettes): updates following the optional Qobs in CreateInputsModel

Refs #60

vignettes/V01_Structure_SD_model.Rmd

@@ -109,7 +109,7 @@ The **airGR** `CreateInputsModel` function is extended in order to handle the `G
 
 
 ```{r}
-InputsModel <- CreateInputsModel(griwrm, DatesR, Precip, PotEvap, Qobs)
+InputsModel <- CreateInputsModel(griwrm, DatesR, Precip, PotEvap)
 ```
 
 # References

vignettes/V02_Calibration_SD_model.Rmd

@@ -47,7 +47,7 @@ PotEvapTot <- cbind(sapply(BasinsObs, function(x) {x$peti}))
 Qobs <- cbind(sapply(BasinsObs, function(x) {x$discharge_spec}))
 Precip <- ConvertMeteoSD(griwrm, PrecipTot)
 PotEvap <- ConvertMeteoSD(griwrm, PotEvapTot)
-InputsModel <- CreateInputsModel(griwrm, DatesR, Precip, PotEvap, Qobs)
+InputsModel <- CreateInputsModel(griwrm, DatesR, Precip, PotEvap)
 str(InputsModel)
 ```
 

vignettes/V03_Open-loop_influenced_flow.Rmd

@@ -69,15 +69,21 @@ BasinsObs <- Severn$BasinsObs
 DatesR <- BasinsObs[[1]]$DatesR
 PrecipTot <- cbind(sapply(BasinsObs, function(x) {x$precipitation}))
 PotEvapTot <- cbind(sapply(BasinsObs, function(x) {x$peti}))
-Qobs <- cbind(sapply(BasinsObs, function(x) {x$discharge_spec}))
 Precip <- ConvertMeteoSD(griwrm, PrecipTot)
 PotEvap <- ConvertMeteoSD(griwrm, PotEvapTot)
+Qobs <- cbind(sapply(BasinsObs, function(x) {x$discharge_spec}))
+```
+
+This time, we need to provide observed flows as inputs for the nodes '54002' and '54095':
+
+```{r}
+QobsInputs <- Qobs[, c("54002", "54095")]
 ```
 
-The `GRiwrmInputsModel` object can be generated taking into account the new `GRiwrm` object:
+Then, the `GRiwrmInputsModel` object can be generated taking into account the new `GRiwrm` object:
 
 ```{r}
-IM_OL <- CreateInputsModel(griwrmV03, DatesR, Precip, PotEvap, Qobs)
+IM_OL <- CreateInputsModel(griwrmV03, DatesR, Precip, PotEvap, QobsInputs)
 ```
 
 ## Calibration of the new model

vignettes/V04_Closed-loop_regulated_withdrawal.Rmd

@@ -231,10 +231,10 @@ for (x in 1:ncol(m))
 As for the previous model, we need to set up an `GRiwrmInputsModel` object containing all the model inputs:
 
 ```{r}
-# A flow is needed for all the nodes in the network
-# even if it is overwritten after by a controller
+# A flow is needed for all direct injection nodes in the network
+# even if they may be overwritten after by a controller
 # The Qobs matrix is completed with 2 new columns for the new nodes
-QobsIrrig <- cbind(Qobs, Irrigation1 = 0, Irrigation2 = 0)
+QobsIrrig <- cbind(Qobs[, c("54002", "54095")], Irrigation1 = 0, Irrigation2 = 0)
 
 # Creation of the GRiwrmInputsModel object
 IM_Irrig <- CreateInputsModel(griwrmV04, DatesR, Precip, PotEvap, QobsIrrig)

vignettes/seinebasin/V01_First_network.Rmd

@@ -80,7 +80,7 @@ The **airGR** CreateInputsModel function is extended in order to handle the griw
 
 
 ```{r CreateInputsModel}
-InputsModel <- CreateInputsModel(griwrm, DatesR, Precip, PotEvap, Qnat)
+InputsModel <- CreateInputsModel(griwrm, DatesR, Precip, PotEvap)
 ```
 
 

vignettes/seinebasin/V04_Open-loop_influenced_flow.Rmd

@@ -195,7 +195,6 @@ Then, we load observation data for each reservoir and each connection:
 library(seinebasin)
 data(QNAT)
 data(Qreservoirs)
-Qnat <- cbind(Qnat, Qreservoirs)
 ```
 
 ## How to handle online reservoir? The Pannecière lake case.
@@ -208,15 +207,15 @@ There are two possibilities:
 If we know in advance the flow released by the reservoir, upstream flow informations is not usefull for the simulation. But reservoir management simulation would need upstream flow informations for simulating the reservoir state during simulation. The second alternative will be useful for the next phases.
 
 ```{r Qnat}
-Qnat <- cbind(Qnat, -Qnat[,"CHAUM_07"] * griwrm2$area[griwrm2$id == "CHAUM_07"] * 1e3)
-colnames(Qnat)[ncol(Qnat)] <- "PANNEC_P"
+Qreservoirs <- cbind(Qreservoirs, -Qnat[,"CHAUM_07"] * griwrm2$area[griwrm2$id == "CHAUM_07"] * 1e3)
+colnames(Qreservoirs)[ncol(Qreservoirs)] <- "PANNEC_P"
 ```
 
 
 ## Create the InputsModel object
 
 ```{r CreateInputsModel}
-InputsModel2 <- CreateInputsModel(griwrm2, DatesR, Precip, PotEvap, Qnat)
+InputsModel2 <- CreateInputsModel(griwrm2, DatesR, Precip, PotEvap, Qreservoirs)
 ```
 
 ## Run simulation with naturalised flow parameters

vignettes/seinebasin/V05_Open-loop_influenced_flow_calibration.Rmd

@@ -48,13 +48,13 @@ data(QOBS)
 iEnd <-which(DatesR == as.POSIXct("2008-07-31", tz = "UTC"))
 
 data(Qreservoirs)
-Qobs3 <- cbind(Qobs, Qreservoirs[1:iEnd,])
+QresMarne <- Qreservoirs[1:iEnd, grep("MARNE", colnames(Qreservoirs))]
 id_GR_nodes <- griwrm3$id[!is.na(griwrm3$model)]
 InputsModel3 <- CreateInputsModel(griwrm3, 
                                   DatesR[1:iEnd], 
                                   Precip[1:iEnd, id_GR_nodes], 
                                   PotEvap[1:iEnd, id_GR_nodes], 
-                                  Qobs3[, griwrm3$id])
+                                  QresMarne)
 ```
 
 ## GriwmRunOptions object
@@ -89,7 +89,7 @@ RunOptions <- CreateRunOptions(
 InputsCrit <- CreateInputsCrit(
   InputsModel = InputsModel3,
   FUN_CRIT = airGR::ErrorCrit_KGE2,
-  RunOptions = RunOptions, Obs = Qobs3[IndPeriod_Run,]
+  RunOptions = RunOptions, Obs = Qobs[IndPeriod_Run,]
 )
 ```
 
@@ -124,7 +124,7 @@ OutputsModels3 <- RunModel(
 htmltools::tagList(lapply(
   griwrm3$id[!is.na(griwrm3$model)],
   function(x) {
-    Q3 <- Qobs3[RunOptions[[1]]$IndPeriod_Run,x]
+    Q3 <- Qobs[RunOptions[[1]]$IndPeriod_Run,x]
     iQ3 <- which(!is.na(Q3))
     IndPeriod_Obs <- iQ3[1]:tail(iQ3,1)
     OutputsModels <- ReduceOutputsModel(OutputsModels3[[x]], IndPeriod_Obs)

vignettes/seinebasin/V05b_Open-loop_influenced_flow_calibration_GR6J.Rmd

@@ -49,13 +49,13 @@ data(QOBS)
 iEnd <-which(DatesR == as.POSIXct("2008-07-31", tz = "UTC"))
 
 data(Qreservoirs)
-Qobs3 <- cbind(Qobs, Qreservoirs[1:iEnd,])
+QresMarne <- Qreservoirs[1:iEnd, grep("MARNE", colnames(Qreservoirs))]
 id_GR_nodes <- griwrm3$id[!is.na(griwrm3$model)]
-InputsModel3 <- CreateInputsModel(griwrm3, 
-                                  DatesR[1:iEnd], 
-                                  Precip[1:iEnd, id_GR_nodes], 
-                                  PotEvap[1:iEnd, id_GR_nodes], 
-                                  Qobs3[, griwrm3$id])
+InputsModel3 <- CreateInputsModel(griwrm3,
+                                  DatesR[1:iEnd],
+                                  Precip[1:iEnd, id_GR_nodes],
+                                  PotEvap[1:iEnd, id_GR_nodes],
+                                  QresMarne)
 ```
 
 ## GriwmRunOptions object
@@ -90,7 +90,7 @@ RunOptions <- CreateRunOptions(
 InputsCrit <- CreateInputsCrit(
   InputsModel = InputsModel3,
   FUN_CRIT = airGR::ErrorCrit_KGE2,
-  RunOptions = RunOptions, Obs = Qobs3[IndPeriod_Run,]
+  RunOptions = RunOptions, Obs = Qobs[IndPeriod_Run,]
 )
 ```
 
@@ -125,7 +125,7 @@ OutputsModels3 <- RunModel(
 htmltools::tagList(lapply(
   griwrm3$id[!is.na(griwrm3$model)],
   function(x) {
-    Q3 <- Qobs3[RunOptions[[1]]$IndPeriod_Run,x]
+    Q3 <- Qobs[RunOptions[[1]]$IndPeriod_Run,x]
     iQ3 <- which(!is.na(Q3))
     IndPeriod_Obs <- iQ3[1]:tail(iQ3,1)
     OutputsModels <- ReduceOutputsModel(OutputsModels3[[x]], IndPeriod_Obs)

vignettes/seinebasin/V06_Naturalised_flow_simulation.Rmd

@@ -59,8 +59,7 @@ data(QNAT)
 InputsModel4 <- CreateInputsModel(griwrm4, 
                                   DatesR, 
                                   Precip[, selectedNodes], 
-                                  PotEvap[, selectedNodes], 
-                                  Qnat[, selectedNodes])
+                                  PotEvap[, selectedNodes])
 ```
 
 ## GriwmRunOptions object