refactor: Remove Girop object dependencies

Closes #9

NAMESPACE

@@ -18,7 +18,6 @@ export(CreateInputsCrit)
 export(CreateInputsModel)
 export(CreateRunOptions)
 export(Ginet)
-export(Girop)
 export(RunModel)
 export(getNodeRanking)
 import(airGR)

R/CreateInputsModel.Griwrm.R

 #' Create InputsModel object for a GRIWRM network
 #'
 #' @param x Ginet object describing the diagram of the semi-distributed model, see \code{[Ginet]}.
-#' @param girop Girop object giving the run-off model parameters, see \code{[Girop]}.
 #' @param DateR Vector of POSIXlt observation time steps.
 #' @param Precip Matrix or data frame of numeric containing precipitation in mm. Column names correspond to node IDs.
 #' @param PotEvap Matrix or data frame of numeric containing potential evaporation in mm. Column names correspond to node IDs.
@@ -11,7 +10,7 @@
 #'
 #' @return GriwrmInputsModel object equivalent to airGR InputsModel object for a semi-distributed model (See \code{\link[airGR]{CreateInputsModel}})
 #' @export
-CreateInputsModel.Griwrm <- function(x, girop, DatesR, Precip, PotEvap, Qobs, verbose = TRUE, ...) {
+CreateInputsModel.Griwrm <- function(x, DatesR, Precip, PotEvap, Qobs, verbose = TRUE, ...) {
 
   InputsModel <- CreateEmptyGriwrmInputsModel()
   Qobs[is.na(Qobs)] <- -99 # airGRCreateInputsModel doesn't accept NA values
@@ -19,7 +18,7 @@ CreateInputsModel.Griwrm <- function(x, girop, DatesR, Precip, PotEvap, Qobs, ve
   for(id in getNodeRanking(x)) {
     if(verbose) cat("CreateInputsModel.griwrm: Treating sub-basin", id, "...\n")
     InputsModel[[id]] <- CreateOneGriwrmInputsModel(
-      id, x, girop, DatesR,Precip[,id], PotEvap[,id], Qobs, ...
+      id, x, DatesR,Precip[,id], PotEvap[,id], Qobs, ...
     )
   }
   return(InputsModel)
@@ -40,16 +39,15 @@ CreateEmptyGriwrmInputsModel <- function() {
 #'
 #' @param id string of the node identifier
 #' @param ginet See \code{[Ginet]}.
-#' @param girop See \code{[Girop]}.
 #' @param DatesR vector of dates required to create the GR model and CemaNeige module inputs.
 #' @param Precip time series of potential evapotranspiration (catchment average) (mm/time step).
 #' @param PotEvap time series of potential evapotranspiration (catchment average) (mm/time step).
 #' @param Qobs Matrix or data frame of numeric containing observed flow (mm/time step). Column names correspond to node IDs.
 ##'
 #' @return \emph{InputsModel} object for one.
-CreateOneGriwrmInputsModel <- function(id, ginet, girop, DatesR, Precip, PotEvap, Qobs) {
+CreateOneGriwrmInputsModel <- function(id, ginet, DatesR, Precip, PotEvap, Qobs) {
   node <- ginet[ginet$id == id,]
-  FUN_MOD <- girop$model[girop$id == id]
+  FUN_MOD <- ginet$model[ginet$id == id]
 
   # Set hydraulic parameters
   UpstreamNodes <- ginet$id[ginet$down == id & !is.na(ginet$down)]
@@ -67,10 +65,10 @@ CreateOneGriwrmInputsModel <- function(id, ginet, girop, DatesR, Precip, PotEvap
         Qupstream <- cbind(Qupstream, Qupstream1)
       }
     }
-    LengthHydro <- ginet$length[girop$id %in% UpstreamNodes]
+    LengthHydro <- ginet$length[ginet$id %in% UpstreamNodes]
     BasinAreas <- c(
-        girop$area[girop$id %in% UpstreamNodes],
-        girop$area[girop$id == id] - sum(girop$area[girop$id %in% UpstreamNodes])
+        ginet$area[ginet$id %in% UpstreamNodes],
+        node$area - sum(ginet$area[ginet$id %in% UpstreamNodes])
     )
   }
 

R/RunModel.GriwrmInputsModel.R

@@ -2,13 +2,13 @@
 #'
 #' @param InputsModel object of class \emph{GriwrmInputsModel}, see \code{[CreateInputsModel.Griwrm]} for details.
 #' @param RunOptions object of class \emph{GriwrmRunOptions}, see \code{[CreateRunOptions.Griwrm]} for details.
-#' @param girop Girop object giving the run-off model parameters, see \code{[Girop]}.
+#' @param Param list of parameter. The list item names are the IDs of the sub-basins. Each item is a vector of numerical parameters.
 #' @param verbose (optional) boolean indicating if the function is run in verbose mode or not, default = \code{TRUE}
 #' @param ... Mandatory for S3 method signature function compatibility with generic.
 #'
 #' @return \emph{GriwrmOutputsModel} object which is a list of \emph{OutputsModel} objects (See \code{\link[airGR]{RunModel}}) for each node of the semi-distributed model.
 #' @export
-RunModel.GriwrmInputsModel <- function(InputsModel, RunOptions, girop, verbose = TRUE, ...) {
+RunModel.GriwrmInputsModel <- function(InputsModel, RunOptions, Param, verbose = TRUE, ...) {
 
   OutputsModel <- list()
   class(OutputsModel) <- append(class(OutputsModel), "GriwrmOutputsModel")
@@ -23,7 +23,7 @@ RunModel.GriwrmInputsModel <- function(InputsModel, RunOptions, girop, verbose =
     OutputsModel[[IM$id]] <- RunModel(
       InputsModel = IM,
       RunOptions = RunOptions[[IM$id]],
-      Param = unlist(girop$params[girop$id == IM$id])
+      Param = Param[[IM$id]]
     )
 
   }

R/ginet.R

@@ -7,8 +7,8 @@
 #'
 #' @return `Ginet` class object containing the description of diagram of the semi-distributed catchment model
 #' @export
-Ginet <- function(db, cols = list(id = "id", down = "down", length = "length", runoff = "runoff"), keep_all = FALSE) {
-  colsDefault <- list(id = "id", down = "down", length = "length", runoff = "runoff")
+Ginet <- function(db, cols = list(id = "id", down = "down", length = "length", model = "model"), keep_all = FALSE) {
+  colsDefault <- list(id = "id", down = "down", length = "length", model = "model", area = "area")
   cols <- utils::modifyList(colsDefault, as.list(cols))
   db <- dplyr::rename(db, unlist(cols))
   if(!keep_all) {

R/girop.R

-#' Generate the list of run-off models and their parameters
-#'
-#' @param db data frame containing at least the id the area and the model of the sub-basin.
-#' @param cols named list or vector for matching columns of `db` parameter. By default, mandatory columns names are: `id`, `area`, `model`. But other names can be handled with a named list or vector containing items defined as `"required name" = "column name in db"`.
-#' @param keep_all Keep all column of `db` or keep only columns defined in `cols`
-#'
-#' @return \emph{Girop} object.
-#' @export
-Girop <- function(db, cols = c(id = "id", area = "area", model = "model", params = "params"), keep_all = FALSE) {
-  colsDefault <- list(id = "id", area = "area", model = "model", params = "params")
-  cols <- utils::modifyList(colsDefault, as.list(cols))
-  if(!any(names(db) == cols$params)) {
-    # Add missing params column in the database
-    db[[cols$params]] = NA
-  }
-  db <- dplyr::rename(db, unlist(cols))
-  if(!keep_all) {
-    db <- dplyr::select(db, names(cols))
-  }
-  class(db) <- append(class(db), "Girop")
-  db
-}

vignettes/V01_First_network.Rmd

@@ -30,52 +30,27 @@ seine_nodes
 
 Create the ginet object which lists the nodes and describes the network diagram. It's a dataframe of class `Ginet` and `Griwrm` with specific column names:
 
-- `id`: the identifier of the node in the network
-- `down`: the identifier of the next node downstream
-- `length`: hydraulic distance to the next downstream node
-- `runoff`: does the node is a rainfall run-off model?
+- `id`: the identifier of the node in the network.
+- `down`: the identifier of the next hydrological node downstream.
+- `length`: hydraulic distance to the next hydrological downstream node.
+- `model`: Name of the hydrological model used (E.g. "RunModel_GR4J"). `NA` for other type of node.
+- `area`: Area of the sub-catchment (km<sup>2</sup>). Used for hydrological model such as GR models. `NA` if not used.
 
 `Ginet` function helps to rename the columns of the dataframe and assign the variable classes.
 
 ```{r}
-# Specify that all nodes are of run-off type
-seine_nodes$runoff <- TRUE
-# Convert distance in km as it the unit used by airGR
-seine_nodes$length <- seine_nodes$distance_aval / 1000
+seine_nodes$model <- "RunModel_GR4J"
 # Generate the ginet object 
-ginet <- Ginet(seine_nodes, list(id = "id_sgl", down = "id_aval"))
+ginet <- Ginet(seine_nodes, list(id = "id_sgl", down = "id_aval", length = "distance_aval"))
 ginet
 ```
 
-Each line of the `Ginet` object having the `runoff` columns switched to `TRUE` should have a corresponding line in the `Girop` object which contains the parameters of the rainfall run-off models. 
-
-The `Girop` object is a dataframe of class `Girop` with specific columns:
-
-- `id`: the identifier of the node in the network
-- `area`: the total area of the basin (including upstream sub-basins) at the location of the node (km<sup>2</sup>)
-- `model`: the name of the rainfall run-off model used (e.g. "RunModel_GR4J")
-- `params`: a list containing the calibration parameters of the model
-
-```{r}
-# Specify which run-off model to use
-seine_nodes$model = "RunModel_GR4J"
-# Generate girop object
-girop <- Girop(seine_nodes, list(id = "id_sgl", area = "area"))
-girop
-```
-
 
 ## Observation time series 
 
 Loading hydrometeorological data on the Seine river basin from the ClimAware project: 
 
 ```{r, warning=FALSE, message=FALSE}
-urls <- 
-  file.path(
-    "https://stratus.irstea.fr/d/0b18e688851a45478f7a/files/?p=/climaware_hydro/Q_OBS_NAT", 
-    paste0(ginet$id, "_NAT.txt&dl=1")
-  )
-names(urls) <- ginet$id
 
 Precip <- NULL
 PotEvap <- NULL
@@ -105,8 +80,8 @@ for(id in ginet$id) {
   Precip <- MergeTS(Precip, id, ts[,c("Date", "Ptot")])
   # ETP column is merged into PotEvap dataframe
   PotEvap <- MergeTS(PotEvap, id, ts[,c("Date", "ETP")])
-  # Convert Qobs from m3/s to mm
-  ts$Qnat <- ts$Qnat * 86.4 / girop$area[girop$id == id]
+  # Convert Qobs from m3/s to mm/time step
+  ts$Qnat <- ts$Qnat * 86.4 / ginet$area[ginet$id == id]
   # Setting data gaps to NA
   ts$Qnat[ts$Qnat <= 0] <- NA
   # Qnat column is merged into Qobs dataframe
@@ -126,7 +101,7 @@ The airGR CreateInputsModel function is extended in order to handle the ginet ob
 
 
 ```{r}
-InputsModel <- CreateInputsModel(ginet, girop, DatesR, Precip, PotEvap, Qobs)
+InputsModel <- CreateInputsModel(ginet, DatesR, Precip, PotEvap, Qobs)
 ```
 
 
@@ -136,6 +111,6 @@ InputsModel <- CreateInputsModel(ginet, girop, DatesR, Precip, PotEvap, Qobs)
 ```{r}
 
 dir.create("_cache", showWarnings = FALSE)
-save(ginet, girop, Qobs, InputsModel, file = "_cache/V01.RData")
+save(ginet, Qobs, InputsModel, file = "_cache/V01.RData")
 ```
 

vignettes/V03_First_Calibration.Rmd

@@ -53,22 +53,19 @@ save(OutputsCalib, file = "_cache/V03.RData")
 ## Run model with Michel calibration
 
 ```{r}
-giropMichel <- girop
-for(id in giropMichel$id) {
-  giropMichel$params[giropMichel$id == id] <- list(OutputsCalib[[id]]$Param)
-}
+ParamMichel <- sapply(ginet$id, function(x) {OutputsCalib[[x]]$Param})
 
 OutputsModels <- RunModel(
   InputsModel = InputsModel,
   RunOptions = RunOptions,
-  girop = giropMichel
+  Param = ParamMichel
 )
 ```
 
 ## Save calibration data for next vignettes
 
 ```{r}
-save(giropMichel, file = "_cache/V03.RData")
+save(ParamMichel, file = "_cache/V03.RData")
 ```
 
 

vignettes/v02_First_run.Rmd

@@ -49,20 +49,22 @@ This lag parameter has to be converted in a speed in m/s used in the airGR lag m
 # Convert TGR routing parameter into speed
 params <- merge(ginet, ClimAwareParams, by.x = "id", by.y = "id_sgl")
 
-for(id in girop$id) {
-  # Maximum connection length with upstream nodes
+ParamClimAware <- sapply(ginet$id, function(id) {
+  nodeParam <- ClimAwareParams[ClimAwareParams$id_sgl == id,]
+  # Record hydrological model parameters
+  Param <- unlist(nodeParam[c("S", "IGF", "KR", "T")])
+  # Add lag model parameter if upstream nodes exist
   UpstrNodes <- which(ginet$down == id & !is.na(ginet$down))
   if(length(UpstrNodes) > 0) {
     maxLength <- max(ginet$length[UpstrNodes])
-    params$LAG <- maxLength * 1000 / ((params$Tau0 + params$K0) * 3600)
-    sLag <- "LAG"
-  } else {
-    sLag <- NULL
+    Param <- c(
+      Param, 
+      maxLength / ((nodeParam$Tau0 + nodeParam$K0) * 3600)
+    )
   }
-  girop$params[girop$id == id] <- list(params[params$id == id, c("S", "IGF", "KR", "T", sLag)])
-}
+  return(Param)
+})
 
-dplyr::select(params, id, S, IGF, KR, T, LAG)
 ```
 
 ## GriwmRunOptions object
@@ -107,14 +109,14 @@ RunOptions <- CreateRunOptions(
 OutputsModelsClimAware <- RunModel(
   InputsModel = InputsModel,
   RunOptions = RunOptions,
-  girop
+  Param = ParamClimAware
 )
 ```
 
 ## Save data for next vignettes
 
 ```{r}
-save(RunOptions, file = "_cache/V02.RData")
+save(RunOptions, ParamClimAware, file = "_cache/V02.RData")
 ```
 
 ## Plot the result for each basin