refactor: rename Ginet to Griwrm

Closes #10

NAMESPACE

@@ -17,7 +17,7 @@ export(CreateCalibOptions)
 export(CreateInputsCrit)
 export(CreateInputsModel)
 export(CreateRunOptions)
-export(Ginet)
+export(Griwrm)
 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 x Griwrm object describing the diagram of the semi-distributed model, see \code{[Griwrm]}.
 #' @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.
@@ -38,19 +38,19 @@ CreateEmptyGriwrmInputsModel <- function() {
 #' Create one InputsModel for a GRIWRM node
 #'
 #' @param id string of the node identifier
-#' @param ginet See \code{[Ginet]}.
+#' @param griwrm See \code{[Griwrm]}.
 #' @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, DatesR, Precip, PotEvap, Qobs) {
-  node <- ginet[ginet$id == id,]
-  FUN_MOD <- ginet$model[ginet$id == id]
+CreateOneGriwrmInputsModel <- function(id, griwrm, DatesR, Precip, PotEvap, Qobs) {
+  node <- griwrm[griwrm$id == id,]
+  FUN_MOD <- griwrm$model[griwrm$id == id]
 
   # Set hydraulic parameters
-  UpstreamNodes <- ginet$id[ginet$down == id & !is.na(ginet$down)]
+  UpstreamNodes <- griwrm$id[griwrm$down == id & !is.na(griwrm$down)]
   Qupstream <- NULL
   LengthHydro <- NULL
   BasinAreas <- NULL
@@ -65,10 +65,10 @@ CreateOneGriwrmInputsModel <- function(id, ginet, DatesR, Precip, PotEvap, Qobs)
         Qupstream <- cbind(Qupstream, Qupstream1)
       }
     }
-    LengthHydro <- ginet$length[ginet$id %in% UpstreamNodes]
+    LengthHydro <- griwrm$length[griwrm$id %in% UpstreamNodes]
     BasinAreas <- c(
-        ginet$area[ginet$id %in% UpstreamNodes],
-        node$area - sum(ginet$area[ginet$id %in% UpstreamNodes])
+        griwrm$area[griwrm$id %in% UpstreamNodes],
+        node$area - sum(griwrm$area[griwrm$id %in% UpstreamNodes])
     )
   }
 

R/Griwrm.R

@@ -5,35 +5,35 @@
 #' @param cols named list or vector for matching columns of `db` parameter. By default, mandatory columns names are: `id`, `down`, `length`. 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 `Ginet` class object containing the description of diagram of the semi-distributed catchment model
+#' @return `Griwrm` 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", model = "model"), keep_all = FALSE) {
+Griwrm <- 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) {
     db <- dplyr::select(db, names(cols))
   }
-  class(db) <- append(class(db), c("Griwrm", "Ginet"))
+  class(db) <- append(class(db), c("Griwrm", "Griwrm"))
   db
 }
 
 #' Sort the nodes from upstream to downstream.
 #'
-#' @param ginet See \code{[Ginet]}.
+#' @param griwrm See \code{[Griwrm]}.
 #'
 #' @return vector with the ordered node names.
 #' @export
-getNodeRanking <- function(ginet) {
-  if(!is(ginet, "Ginet")) {
-    stop("getNodeRanking: ginet argument should be of class Ginet")
+getNodeRanking <- function(griwrm) {
+  if(!is(griwrm, "Griwrm")) {
+    stop("getNodeRanking: griwrm argument should be of class Griwrm")
   }
   # Rank 1
-  rank <- setdiff(ginet$id, ginet$down)
+  rank <- setdiff(griwrm$id, griwrm$down)
   ranking <- rank
   # Next ranks
-  while(any(ginet$id %in% rank)) {
-    rank <- ginet$down[ginet$id %in% rank]
+  while(any(griwrm$id %in% rank)) {
+    rank <- griwrm$down[griwrm$id %in% rank]
     ranking <- c(ranking, rank)
   }
   ranking <- unique(ranking, fromLast = TRUE)

vignettes/V01_First_network.Rmd

@@ -22,13 +22,13 @@ List of nodes
 
 ```{r}
 seine_nodes <- readr::read_delim(
-  file = system.file("seine_data", "network_gauging_stations.txt", package = "griwrm"), 
+  file = system.file("seine_data", "network_gauging_stations.txt", package = "griwrm"),
   delim = "\t"
 )
 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:
+Create the griwrm object which lists the nodes and describes the network diagram. It's a dataframe of class `Griwrm` and `Griwrm` with specific column names:
 
 - `id`: the identifier of the node in the network.
 - `down`: the identifier of the next hydrological node downstream.
@@ -36,25 +36,25 @@ Create the ginet object which lists the nodes and describes the network diagram.
 - `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.
+`Griwrm` function helps to rename the columns of the dataframe and assign the variable classes.
 
 ```{r}
 seine_nodes$model <- "RunModel_GR4J"
-# Generate the ginet object 
-ginet <- Ginet(seine_nodes, list(id = "id_sgl", down = "id_aval", length = "distance_aval"))
-ginet
+# Generate the griwrm object
+griwrm <- Griwrm(seine_nodes, list(id = "id_sgl", down = "id_aval", length = "distance_aval"))
+griwrm
 ```
 
 
-## Observation time series 
+## Observation time series
 
-Loading hydrometeorological data on the Seine river basin from the ClimAware project: 
+Loading hydrometeorological data on the Seine river basin from the ClimAware project:
 
 ```{r, warning=FALSE, message=FALSE}
 
 Precip <- NULL
 PotEvap <- NULL
-Qobs <- NULL 
+Qobs <- NULL
 
 MergeTS <- function(dfOld, id, dfNew) {
     names(dfNew) <- c("DatesR", id) # Renaming columns of the new input into date and sub-basin ID
@@ -66,13 +66,13 @@ MergeTS <- function(dfOld, id, dfNew) {
   return(dfOut)
 }
 
-for(id in ginet$id) {
-  url <- 
+for(id in griwrm$id) {
+  url <-
     file.path(
-      "https://stratus.irstea.fr/d/0b18e688851a45478f7a/files/?p=/climaware_hydro/Q_OBS_NAT", 
+      "https://stratus.irstea.fr/d/0b18e688851a45478f7a/files/?p=/climaware_hydro/Q_OBS_NAT",
       paste0(id, "_NAT.txt&dl=1")
     )
-  ts <- readr::read_delim(file = url, 
+  ts <- readr::read_delim(file = url,
                           delim = ";", skip = 16, trim_ws = TRUE)
   # Date conversion to POSIX
   ts$Date <- as.POSIXlt(lubridate::ymd(ts$Date))
@@ -81,7 +81,7 @@ for(id in ginet$id) {
   # ETP column is merged into PotEvap dataframe
   PotEvap <- MergeTS(PotEvap, id, ts[,c("Date", "ETP")])
   # Convert Qobs from m3/s to mm/time step
-  ts$Qnat <- ts$Qnat * 86.4 / ginet$area[ginet$id == id]
+  ts$Qnat <- ts$Qnat * 86.4 / griwrm$area[griwrm$id == id]
   # Setting data gaps to NA
   ts$Qnat[ts$Qnat <= 0] <- NA
   # Qnat column is merged into Qobs dataframe
@@ -97,11 +97,11 @@ Qobs$DateR <- NULL
 
 The GRIWRM InputsModel object is a list of airGR InputsModel. The identifier of the sub-basin is used as key in the list which is ordered from upstream to downstream.
 
-The airGR CreateInputsModel function is extended in order to handle the ginet object which describe the basin diagram:
+The airGR CreateInputsModel function is extended in order to handle the griwrm object which describe the basin diagram:
 
 
 ```{r}
-InputsModel <- CreateInputsModel(ginet, DatesR, Precip, PotEvap, Qobs)
+InputsModel <- CreateInputsModel(griwrm, DatesR, Precip, PotEvap, Qobs)
 ```
 
 
@@ -111,6 +111,6 @@ InputsModel <- CreateInputsModel(ginet, DatesR, Precip, PotEvap, Qobs)
 ```{r}
 
 dir.create("_cache", showWarnings = FALSE)
-save(ginet, Qobs, InputsModel, file = "_cache/V01.RData")
+save(griwrm, Qobs, InputsModel, file = "_cache/V01.RData")
 ```
 

vignettes/V03_First_Calibration.Rmd

@@ -25,7 +25,7 @@ load("_cache/V02.RData")
 
 ```{r}
 InputsCrit <- CreateInputsCrit(
-  InputsModel = InputsModel, 
+  InputsModel = InputsModel,
   FUN_CRIT = airGR::ErrorCrit_KGE2,
   RunOptions = RunOptions, Qobs = Qobs
 )
@@ -53,7 +53,7 @@ save(OutputsCalib, file = "_cache/V03.RData")
 ## Run model with Michel calibration
 
 ```{r}
-ParamMichel <- sapply(ginet$id, function(x) {OutputsCalib[[x]]$Param})
+ParamMichel <- sapply(griwrm$id, function(x) {OutputsCalib[[x]]$Param})
 
 OutputsModels <- RunModel(
   InputsModel = InputsModel,
@@ -73,7 +73,7 @@ save(ParamMichel, file = "_cache/V03.RData")
 
 ```{r, fig.height = 5, fig.width = 8}
 htmltools::tagList(lapply(
-  names(OutputsModels), 
+  names(OutputsModels),
   function(x) {
     plot(OutputsModels[[x]], Qobs = Qobs[RunOptions[[x]]$IndPeriod_Run,x] , main = x)
   }

vignettes/v02_First_run.Rmd

@@ -28,7 +28,7 @@ Run `vignette("01_First_network", package = "griwrm")` before this one in order
 load("_cache/V01.RData")
 ```
 
-### Loading 
+### Loading
 
 Data comes from calibration of ClimAware project with naturalised flows.
 
@@ -40,25 +40,25 @@ ClimAwareParams <- readr::read_csv(
 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. 
+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 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:
 
 ```{r}
 # Convert TGR routing parameter into speed
-params <- merge(ginet, ClimAwareParams, by.x = "id", by.y = "id_sgl")
+params <- merge(griwrm, ClimAwareParams, by.x = "id", by.y = "id_sgl")
 
-ParamClimAware <- sapply(ginet$id, function(id) {
+ParamClimAware <- sapply(griwrm$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$down))
+  UpstrNodes <- which(griwrm$down == id & !is.na(griwrm$down))
   if(length(UpstrNodes) > 0) {
-    maxLength <- max(ginet$length[UpstrNodes])
+    maxLength <- max(griwrm$length[UpstrNodes])
     Param <- c(
-      Param, 
+      Param,
       maxLength / ((nodeParam$Tau0 + nodeParam$K0) * 3600)
     )
   }
@@ -82,7 +82,7 @@ library(lubridate)
 IndPeriod_Run <- seq(
   which(InputsModel[[1]]$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:
@@ -95,8 +95,8 @@ IndPeriod_WarmUp = seq(1,IndPeriod_Run[1]-1)
 
 ```{r}
 RunOptions <- CreateRunOptions(
-  InputsModel = InputsModel, 
-  IndPeriod_WarmUp = IndPeriod_WarmUp, 
+  InputsModel = InputsModel,
+  IndPeriod_WarmUp = IndPeriod_WarmUp,
   IndPeriod_Run = IndPeriod_Run
 )
 ```
@@ -123,7 +123,7 @@ save(RunOptions, ParamClimAware, file = "_cache/V02.RData")
 
 ```{r, fig.height = 5, fig.width = 8}
 htmltools::tagList(lapply(
-  names(OutputsModelsClimAware), 
+  names(OutputsModelsClimAware),
   function(x) {
     plot(OutputsModelsClimAware[[x]], Qobs = Qobs[IndPeriod_Run,x] , main = x)
   }