refactor: rename 'Griwrm' to 'GRiwrm' in the code

Refs #15

R/Calibration.GriwrmInputsModel.R

 #' Calibration of a semi-distributed run-off model
 #'
-#' @param InputsModel object of class \emph{GriwrmInputsModel}, see \code{\link{CreateInputsModel.GRiwrm}} for details.
-#' @param RunOptions object of class \emph{GriwrmRunOptions}, see \code{\link{CreateRunOptiosn.GRiwrm}} for details.
-#' @param InputsCrit object of class \emph{GriwrmInputsCrit}, see \code{\link{CreateInputsCrit.GRiwrm}} for details.
-#' @param CalibOptions object of class \emph{GriwrmCalibOptions}, see \code{\link{CreateCalibOptions.GRiwrm}} for details.
+#' @param InputsModel object of class \emph{GRiwrmInputsModel}, see \code{\link{CreateInputsModel.GRiwrm}} for details.
+#' @param RunOptions object of class \emph{GRiwrmRunOptions}, see \code{\link{CreateRunOptiosn.GRiwrm}} for details.
+#' @param InputsCrit object of class \emph{GRiwrmInputsCrit}, see \code{\link{CreateInputsCrit.GRiwrm}} for details.
+#' @param CalibOptions object of class \emph{GRiwrmCalibOptions}, see \code{\link{CreateCalibOptions.GRiwrm}} for details.
 #' @param useUpstreamQsim boolean describing if simulated (\code{TRUE}) or observed (\code{FALSE}) flows are used for calibration. Default is \code{TRUE}.
 #' @param verbose (optional) boolean indicating if the function is run in verbose mode or not, default = \code{TRUE}
 #' @param ... further arguments passed to \code{\link[airGR]{Calibration}}.
 #'
-#' @return GriwrmOutputsCalib object which is a list of OutputsCalib (See \code{\link[airGR]{Calibration}}) for each node of the semi-distributed model.
+#' @return GRiwrmOutputsCalib object which is a list of OutputsCalib (See \code{\link[airGR]{Calibration}}) for each node of the semi-distributed model.
 #' @export
-Calibration.GriwrmInputsModel <- function(InputsModel,
+Calibration.GRiwrmInputsModel <- function(InputsModel,
                                           RunOptions,
                                           InputsCrit,
                                           CalibOptions,
@@ -19,13 +19,13 @@ Calibration.GriwrmInputsModel <- function(InputsModel,
                                           ...) {
 
   OutputsCalib <- list()
-  class(OutputsCalib) <- append(class(OutputsCalib), "GriwrmOutputsCalib")
+  class(OutputsCalib) <- append(class(OutputsCalib), "GRiwrmOutputsCalib")
 
   OutputsModel <- list()
-  class(OutputsModel) <- append(class(OutputsModel), "GriwrmOutputsModel")
+  class(OutputsModel) <- append(class(OutputsModel), "GRiwrmOutputsModel")
 
   for(IM in InputsModel) {
-    if(verbose) cat("Calibration.GriwrmInputsModel: Treating sub-basin", IM$id, "...\n")
+    if(verbose) cat("Calibration.GRiwrmInputsModel: Treating sub-basin", IM$id, "...\n")
 
     if(useUpstreamQsim) {
       # Update InputsModel$Qupstream with simulated upstream flows

R/Calibration.R

@@ -3,7 +3,7 @@
 #' @param InputsModel the class of the first parameter determine which calibration is used
 #' @param ... further arguments passed to or from other methods.
 #'
-#' @return \emph{OutputsCalib} or \emph{GriwrmOutputsCalib} object
+#' @return \emph{OutputsCalib} or \emph{GRiwrmOutputsCalib} object
 #' @export
 Calibration <- function(InputsModel, ...) {
   UseMethod("Calibration", InputsModel)

R/CreateCalibOptions.GriwrmInputsModel.R

 #' Title
 #'
-#' @param InputsModel object of class \emph{GriwrmInputsModel}, see \code{\link{CreateInputsModel.GRiwrm}} for details.
+#' @param InputsModel object of class \emph{GRiwrmInputsModel}, see \code{\link{CreateInputsModel.GRiwrm}} for details.
 #' @param ... further arguments passed to \code{\link[airGR]{CreateCalibOptions}}.
 #'
-#' @return \emph{GriwrmCalibOptions} object.
+#' @return \emph{GRiwrmCalibOptions} object.
 #' @export
-CreateCalibOptions.GriwrmInputsModel <- function(InputsModel, ...) {
+CreateCalibOptions.GRiwrmInputsModel <- function(InputsModel, ...) {
 
   CalibOptions <- list()
 

R/CreateInputsCrit.GriwrmInputsModel.R

-#' Create \emph{GriwrmInputsCrit} object for GR-IWRM.
-#' @param InputsModel  object of class \emph{GriwrmInputsModel}, see \code{\link{CreateInputsModel.GRiwrm}} for details.
+#' Create \emph{GRiwrmInputsCrit} object for GR-IWRM.
+#' @param InputsModel  object of class \emph{GRiwrmInputsModel}, see \code{\link{CreateInputsModel.GRiwrm}} for details.
 #' @param FUN_CRIT \[function (atomic or list)\] error criterion function (e.g. \code{\link[airGR]{ErrorCrit_RMSE}}, \code{\link[airGR]{ErrorCrit_NSE}})
-#' @param RunOptions object of class \emph{GriwrmRunOptions}, see \code{[CreateRunOptions.GRiwrm]} for details.
+#' @param RunOptions object of class \emph{GRiwrmRunOptions}, see \code{[CreateRunOptions.GRiwrm]} for details.
 #' @param Qobs matrix or data frame containing observed flows. Column names correspond to nodes ID
 #' @param ... further arguments passed to \code{\link[airGR]{CreateInputsCrit}}.
 #'
-#' @return Object of class \emph{GriwrmInputsCrit}
+#' @return Object of class \emph{GRiwrmInputsCrit}
 #' @export
-CreateInputsCrit.GriwrmInputsModel <- function(InputsModel,
+CreateInputsCrit.GRiwrmInputsModel <- function(InputsModel,
                                                FUN_CRIT = airGR::ErrorCrit_NSE,
                                                RunOptions,
                                                Qobs,
                                                ...) {
   InputsCrit <- list()
-  class(InputsCrit) <- append(class(InputsCrit), "GriwrmInputsCrit")
+  class(InputsCrit) <- append(class(InputsCrit), "GRiwrmInputsCrit")
 
   for(IM in InputsModel) {
     InputsCrit[[IM$id]] <- CreateInputsCrit.InputsModel(

R/CreateInputsModel.Griwrm.R

@@ -8,16 +8,16 @@
 #' @param verbose (optional) boolean indicating if the function is run in verbose mode or not, default = \code{TRUE}
 #' @param ... further arguments passed to \code{\link[airGR]{CreateInputsModel}}.
 #'
-#' @return GriwrmInputsModel object equivalent to airGR InputsModel object for a semi-distributed model (See \code{\link[airGR]{CreateInputsModel}})
+#' @return GRiwrmInputsModel object equivalent to airGR InputsModel object for a semi-distributed model (See \code{\link[airGR]{CreateInputsModel}})
 #' @export
 CreateInputsModel.GRiwrm <- function(x, DatesR, Precip, PotEvap, Qobs, verbose = TRUE, ...) {
 
-  InputsModel <- CreateEmptyGriwrmInputsModel()
+  InputsModel <- CreateEmptyGRiwrmInputsModel()
   Qobs[is.na(Qobs)] <- -99 # airGRCreateInputsModel doesn't accept NA values
 
   for(id in getNodeRanking(x)) {
     if(verbose) cat("CreateInputsModel.griwrm: Treating sub-basin", id, "...\n")
-    InputsModel[[id]] <- CreateOneGriwrmInputsModel(
+    InputsModel[[id]] <- CreateOneGRiwrmInputsModel(
       id, x, DatesR,Precip[,id], PotEvap[,id], Qobs, ...
     )
   }
@@ -27,10 +27,10 @@ CreateInputsModel.GRiwrm <- function(x, DatesR, Precip, PotEvap, Qobs, verbose =
 
 #' Create an empty InputsModel object for GRIWRM nodes
 #'
-#' @return \emph{GriwrmInputsModel} empty object
-CreateEmptyGriwrmInputsModel <- function() {
+#' @return \emph{GRiwrmInputsModel} empty object
+CreateEmptyGRiwrmInputsModel <- function() {
   InputsModel <- list()
-  class(InputsModel) <- append(class(InputsModel), "GriwrmInputsModel")
+  class(InputsModel) <- append(class(InputsModel), "GRiwrmInputsModel")
   return(InputsModel)
 }
 
@@ -45,7 +45,7 @@ CreateEmptyGriwrmInputsModel <- function() {
 #' @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, griwrm, DatesR, Precip, PotEvap, Qobs) {
+CreateOneGRiwrmInputsModel <- function(id, griwrm, DatesR, Precip, PotEvap, Qobs) {
   node <- griwrm[griwrm$id == id,]
   FUN_MOD <- griwrm$model[griwrm$id == id]
 

R/CreateInputsModel.R

@@ -3,7 +3,7 @@
 #' @param x First parameter determining which InputsModel object is created
 #' @param ... further arguments passed to or from other methods.
 #'
-#' @return InputsModel or GriwrmInputsObject object
+#' @return InputsModel or GRiwrmInputsObject object
 #' @export
 CreateInputsModel <- function(x, ...) {
   UseMethod("CreateInputsModel", x)

R/CreateRunOptions.GriwrmInputsModel.R

-#' Create \emph{GriwrmRunOptions} object for running and calibrating model in GR-IWRM.
+#' Create \emph{GRiwrmRunOptions} object for running and calibrating model in GR-IWRM.
 #'
-#' @param InputsModel object of class \emph{GriwrmInputsModel}, see \code{\link{CreateInputsModel.GRiwrm}} for details.
+#' @param InputsModel object of class \emph{GRiwrmInputsModel}, see \code{\link{CreateInputsModel.GRiwrm}} for details.
 #' @param ... further arguments passed to \code{\link[airGR]{CreateOptions}}.
 #'
-#' @return \emph{GriwrmRunOptions} object for running and calibrating model in GR-IWRM.
+#' @return \emph{GRiwrmRunOptions} object for running and calibrating model in GR-IWRM.
 #' @export
-CreateRunOptions.GriwrmInputsModel <- function(InputsModels, ...) {
+CreateRunOptions.GRiwrmInputsModel <- function(InputsModels, ...) {
 
   RunOptions <- list()
-  class(RunOptions) <- append(class(RunOptions), "GriwrmRunOptions")
+  class(RunOptions) <- append(class(RunOptions), "GRiwrmRunOptions")
 
   for(InputsModelBasin in InputsModels) {
     RunOptions[[InputsModelBasin$id]] <- CreateRunOptions(InputsModel = InputsModelBasin, ...)

R/CreateRunOptions.R

-#' Create \emph{RunOptions} object for airGR and GR-IWRM. See \code{\link[airGR]{CreateOptions}} and \code{[CreateOptions.GriwrmInputsModel]}.
+#' Create \emph{RunOptions} object for airGR and GR-IWRM. See \code{\link[airGR]{CreateOptions}} and \code{[CreateOptions.GRiwrmInputsModel]}.
 #'
-#' @param InputsModel object of class \emph{InputsModel} (see \code{\link[airGR]{CreateInputsModel}}) or \emph{GriwrmInputsModel} (See \code{[CreateInputsModel.GRiwrm]}).
+#' @param InputsModel object of class \emph{InputsModel} (see \code{\link[airGR]{CreateInputsModel}}) or \emph{GRiwrmInputsModel} (See \code{[CreateInputsModel.GRiwrm]}).
 #' @param ... further arguments passed to or from other methods.
 #'
 #' @return Object of \emph{RunOptions} class family

R/DiagramGriwrm.R

@@ -14,12 +14,12 @@
 #' @examples
 #' \dontrun{
 #' # Display diagram
-#' DiagramGriwrm(griwrm)
+#' DiagramGRiwrm(griwrm)
 #' # Is the same as
-#' DiagrammeR::mermaid(DiagramGriwrm(griwrm, display = FALSE), width = "100%", height = "100%")
+#' DiagrammeR::mermaid(DiagramGRiwrm(griwrm, display = FALSE), width = "100%", height = "100%")
 #' }
 #'
-DiagramGriwrm <- function(griwrm, display = TRUE, orientation = "LR") {
+DiagramGRiwrm <- function(griwrm, display = TRUE, orientation = "LR") {
   if(Sys.getenv("RSTUDIO") != "1") {
     return()
   }

R/RunModel.GriwrmInputsModel.R

 #' Title
 #'
-#' @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 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 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.
+#' @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, Param, verbose = TRUE, ...) {
+RunModel.GRiwrmInputsModel <- function(InputsModel, RunOptions, Param, verbose = TRUE, ...) {
 
   OutputsModel <- list()
-  class(OutputsModel) <- append(class(OutputsModel), "GriwrmOutputsModel")
+  class(OutputsModel) <- append(class(OutputsModel), "GRiwrmOutputsModel")
 
   for(IM in InputsModel) {
-    if(verbose) cat("RunModel.GriwrmInputsModel: Treating sub-basin", IM$id, "...\n")
+    if(verbose) cat("RunModel.GRiwrmInputsModel: Treating sub-basin", IM$id, "...\n")
 
     # Update InputsModel$Qupstream with simulated upstream flows
     IM <- UpdateQsimUpstream(IM, RunOptions[[IM$id]]$IndPeriod_Run, OutputsModel)

R/RunModel.R

-#' RunModel function for both airGR and GriwrmInputsModel object
+#' RunModel function for both airGR and GRiwrmInputsModel object
 #'
 #' @param InputsModel object of class \emph{InputsModel}, see \code{\link[airGR]{CreateInputsModel}} for details.
 #' @param ... further arguments passed to or from other methods.

R/UpdateQsimUpstream.R

-#' Update InputsModel$Qupstream with simulated upstream flows provided by GriwrmOutputsModels object.
+#' Update InputsModel$Qupstream with simulated upstream flows provided by GRiwrmOutputsModels object.
 #'
-#' @param InputsModel \emph{GriwrmInputsModel} object. See \code{[CreateInputsModel.GRiwrm]}.
+#' @param InputsModel \emph{GRiwrmInputsModel} object. See \code{[CreateInputsModel.GRiwrm]}.
 #' @param IndPeriod_Run numeric index of period to be used for the model run (-)
-#' @param OutputsModel \emph{GriwrmOutputsModel} object provided by \code{[RunModel.GriwrmInputsModel]}.
+#' @param OutputsModel \emph{GRiwrmOutputsModel} object provided by \code{[RunModel.GRiwrmInputsModel]}.
 #'
-#' @description This function is used by \code{\link{RunModel.GriwrmInputsModel}} and \code{\link{Calibration.GriwrmInputsModel}} in order to provide upstream simulated flows to a node.
+#' @description This function is used by \code{\link{RunModel.GRiwrmInputsModel}} and \code{\link{Calibration.GRiwrmInputsModel}} in order to provide upstream simulated flows to a node.
 #'
 #' @return InputsModel object with updated QobsUpsr
 #'

vignettes/V01_First_network.Rmd

@@ -48,7 +48,7 @@ griwrm
 The diagram of the network structure is represented below with in blue the upstream nodes with a GR4J model and in green the intermediate nodes with an SD (GR4J + LAG) model.
 
 ```{r fig.height = 7, fig.width = 8}
-DiagramGriwrm(griwrm)
+DiagramGRiwrm(griwrm)
 ```
 
 

vignettes/V03_First_Calibration.Rmd

@@ -32,7 +32,7 @@ InputsCrit <- CreateInputsCrit(
 str(InputsCrit)
 ```
 
-## GriwrmCalibOptions object
+## GRiwrmCalibOptions object
 
 ```{r}
 CalibOptions <- CreateCalibOptions(InputsModel)

vignettes/V04_Open-loop_influenced_flow.Rmd

@@ -177,7 +177,7 @@ Reservoir connections are added to the GRiwrm object:
 reservoir_connections$model <- NA
 reservoir_connections$area <- NA
 griwrm2 <- rbind(griwrm, reservoir_connections)
-DiagramGriwrm(griwrm2)
+DiagramGRiwrm(griwrm2)
 ```
 
 

vignettes/V05_Open-loop_influenced_flow_calibration.Rmd

@@ -36,10 +36,10 @@ Remove extra items from global configuration
 selectedNodes <- c("MARNE_P23", "STDIZ_04", "LOUVE_19", "VITRY_25", "MARNE_P28", "MARNE_R25", "CHALO_21", "MONTR_18", "NOISI_17")
 griwrm3 <- griwrm2[griwrm2$id %in% selectedNodes,]
 griwrm3[griwrm3$id == "NOISI_17", c("down", "length")] = NA # Downstream station instead of PARIS_05
-DiagramGriwrm(griwrm3)
+DiagramGRiwrm(griwrm3)
 ```
 
-Generate `GriwrmInputsModel` object
+Generate `GRiwrmInputsModel` object
 
 ```{r}
 Qobs3 <- cbind(Qobs2, QobsReservoirs)
@@ -83,7 +83,7 @@ InputsCrit <- CreateInputsCrit(
 )
 ```
 
-## GriwrmCalibOptions object
+## GRiwrmCalibOptions object
 
 ```{r}
 CalibOptions <- CreateCalibOptions(InputsModel3)