Merge branch '7-remove-gits-class-object-and-use-createinputsmodel-directly' into 'master'

Resolve "Remove Gits class object and use CreateInputsModel directly" Closes #9, #10, and #7 See merge request in-wop/griwrm!3

Merge branch '7-remove-gits-class-object-and-use-createinputsmodel-directly' into 'master'
Resolve "Remove Gits class object and use CreateInputsModel directly" Closes #9, #10, and #7 See merge request in-wop/griwrm!3
2ead268e · Dorchies David · acd2d917 · cee0dca3 · 2ead268e · 2ead268e
Commit 2ead268e authored 4 years ago by Dorchies David
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+158 -251
--- a/.Rbuildignore
+++ b/.Rbuildignore
 ^griwrm\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
-\.gitlab-ci\.yml
-R_LIBS
+^\.gitlab-ci\.yml$
+^R_LIBS
+^vignettes/_cache
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@
 # Man pages generated by Roxygen
 man/*.Rd
 /.vscode/
+/NAMESPACE

 ###############################################################################


--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -20,12 +20,15 @@ update_packages:
  script:
    - mkdir -p R_LIBS
    - Rscript -e 'if(!dir.exists("R_LIBS/remotes")) install.packages("remotes", lib = "R_LIBS")'
-    - Rscript -e 'remotes::update_packages(c("dplyr", "rmarkdown", "readr", "lubridate", "zoo"), lib = "R_LIBS")'
+    - apt-get update && apt-get -y install libxml2-dev
+    - Rscript -e 'remotes::update_packages(c("dplyr", "rmarkdown", "readr", "lubridate", "zoo", "roxygen2"), lib = "R_LIBS")'
    - Rscript -e 'remotes::install_gitlab("HYCAR-Hydro/airgr@sd", host = "gitlab.irstea.fr", lib = "R_LIBS")'

 build:
  stage: build
  script:
+    - apt-get update && apt-get -y install libxml2-dev
+    - Rscript -e "roxygen2::roxygenise()"
    - R CMD build ../griwrm
  artifacts:
    paths:

--- a/DESCRIPTION
+++ b/DESCRIPTION
 Package: griwrm
 Title: GR based Integrated Water Resource Management
-Version: 0.2.0
+Version: 0.2.1
 Authors@R:
    person(given = "David",
           family = "Dorchies",

--- a/NAMESPACE
+++ b/NAMESPACE
-# Generated by roxygen2: do not edit by hand
-
-S3method(Calibration,GriwrmInputsModel)
-S3method(Calibration,InputsModel)
-S3method(CreateCalibOptions,GriwrmInputsModel)
-S3method(CreateCalibOptions,InputsModel)
-S3method(CreateInputsCrit,GriwrmInputsModel)
-S3method(CreateInputsCrit,InputsModel)
-S3method(CreateInputsModel,Griwrm)
-S3method(CreateInputsModel,default)
-S3method(CreateRunOptions,GriwrmInputsModel)
-S3method(CreateRunOptions,InputsModel)
-S3method(RunModel,GriwrmInputsModel)
-S3method(RunModel,InputsModel)
-S3method(merge,Gits)
-export(Calibration)
-export(CreateCalibOptions)
-export(CreateInputsCrit)
-export(CreateInputsModel)
-export(CreateRunOptions)
-export(Ginet)
-export(Girop)
-export(Gits)
-export(RunModel)
-export(getNodeRanking)
-import(airGR)
--- a/R/Calibration.InputsModel.R
+++ b/R/Calibration.InputsModel.R
-#' Wrapper to \code{\link[airGR]{Calibration}}.
+#' Wrapper to \code{\link[airGR]{Calibration}} for one sub-basin.
 #'
-#' @param InputsModel object of class \emph{InputsModel}, see \code{\link[airGR]{CreateInputsModel}} for details.
-#' @param ... further arguments passed to \code{\link[airGR]{Calibration}}.
-#'
-#' @return \emph{CalibOutput} object.
+#' @inherit airGR::Calibration
 #' @export
 Calibration.InputsModel <- function(InputsModel, ...) {
  airGR::Calibration(InputsModel, FUN_MOD = InputsModel$FUN_MOD, ...)

--- a/R/CreateCalibOptions.InputsModel.R
+++ b/R/CreateCalibOptions.InputsModel.R
-#' Wrapper to \code{\link[airGR]{CreateCalibOptions}}
+#' Wrapper to \code{\link[airGR]{CreateCalibOptions}} for one sub-basin.
 #'
-#' @param InputsModel object of class \emph{InputsModel}, see \code{\link[airGR]{CreateInputsModel}} for details.
-#' @param ... further arguments passed to \code{\link[airGR]{CreateCalibOptions}}.
-#'
-#' @return \emph{CalibOptions} object.
+#' @inherit airGR::CreateCalibOptions
 #' @export
 CreateCalibOptions.InputsModel <- function(InputsModel,
                               ...) {

--- a/R/CreateInputsCrit.GriwrmInputsModel.R
+++ b/R/CreateInputsCrit.GriwrmInputsModel.R
@@ -2,7 +2,7 @@
 #' @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 gits object of class \emph{Gits}, see [Gits].
+#' @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}
@@ -10,7 +10,7 @@
 CreateInputsCrit.GriwrmInputsModel <- function(InputsModel,
                                               FUN_CRIT = airGR::ErrorCrit_NSE,
                                               RunOptions,
-                                               gits,
+                                               Qobs,
                                               ...) {
  InputsCrit <- list()
  class(InputsCrit) <- append(class(InputsCrit), "GriwrmInputsCrit")
@@ -20,7 +20,7 @@ CreateInputsCrit.GriwrmInputsModel <- function(InputsModel,
      InputsModel = IM,
      FUN_CRIT = FUN_CRIT,
      RunOptions = RunOptions[[IM$id]],
-      Obs = gits[[IM$id]]$Qobs[RunOptions[[IM$id]]$IndPeriod_Run],
+      Obs = Qobs[RunOptions[[IM$id]]$IndPeriod_Run, IM$id],
      ...
    )
  }

--- a/R/CreateInputsCrit.InputsModel.R
+++ b/R/CreateInputsCrit.InputsModel.R
-#' Wrapper to \code{\link[airGR]{CreateInputsCrit}}
+#' Wrapper to \code{\link[airGR]{CreateInputsCrit}} for one sub-basin.
 #'
-#' @param InputsModel object of class \emph{InputsModel}, see \code{\link[airGR]{CreateInputsModel}} 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 ... further arguments passed to \code{\link[airGR]{CreateInputsCrit}}
-#'
-#' @return object of class \emph{InputsCrit} containing the data required to evaluate the model outputs. See \code{\link[airGR]{CreateInputsCrit}}
+#' @inherit airGR::CreateInputsCrit
 #' @export
 CreateInputsCrit.InputsModel <- function(InputsModel,
                                         FUN_CRIT,

--- a/R/CreateInputsModel.Griwrm.R
+++ b/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 gits Gits object giving the observation time series, see \code{[Gits]}.
+#' @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.
+#' @param Qobs Matrix or data frame of numeric containing potential observed flow in mm. Column names correspond to node IDs.
 #' @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}})
 #' @export
-CreateInputsModel.Griwrm <- function(x, girop, gits, 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

  for(id in getNodeRanking(x)) {
    if(verbose) cat("CreateInputsModel.griwrm: Treating sub-basin", id, "...\n")
-    InputsModel[[id]] <- CreateOneGriwrmInputsModel(id, x, girop, gits, ...)
+    InputsModel[[id]] <- CreateOneGriwrmInputsModel(
+      id, x, DatesR,Precip[,id], PotEvap[,id], Qobs, ...
+    )
  }
  return(InputsModel)
 }
@@ -33,17 +38,19 @@ CreateEmptyGriwrmInputsModel <- function() {
 #' Create one InputsModel for a GRIWRM node
 #'
 #' @param id string of the node identifier
-#' @param ginet See \code{[Ginet]}.
-#' @param girop See \code{[Girop]}.
-#' @param gits See \code{[Gits]}.
-#'
+#' @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, girop, gits) {
-  node <- ginet[ginet$id == id,]
-  FUN_MOD <- girop$model[girop$id == id]
+CreateOneGriwrmInputsModel <- function(id, griwrm, DatesR, Precip, PotEvap, Qobs) {
+  node <- griwrm[griwrm$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
@@ -51,26 +58,26 @@ CreateOneGriwrmInputsModel <- function(id, ginet, girop, gits) {
  if(length(UpstreamNodes) > 0) {
    # Sub-basin with hydraulic routing
    for(idUpstrNode in UpstreamNodes) {
-      Qupstream1 <- matrix(gits[[idUpstrNode]]$Qobs, ncol = 1)
+      Qupstream1 <- matrix(Qobs[,idUpstrNode], ncol = 1)
      if(is.null(Qupstream)) {
        Qupstream <- Qupstream1
      } else {
        Qupstream <- cbind(Qupstream, Qupstream1)
      }
    }
-    LengthHydro <- ginet$length[girop$id %in% UpstreamNodes]
+    LengthHydro <- griwrm$length[griwrm$id %in% UpstreamNodes]
    BasinAreas <- c(
-        girop$area[girop$id %in% UpstreamNodes],
-        girop$area[girop$id == id] - sum(girop$area[girop$id %in% UpstreamNodes])
+        griwrm$area[griwrm$id %in% UpstreamNodes],
+        node$area - sum(griwrm$area[griwrm$id %in% UpstreamNodes])
    )
  }

  # Set model inputs with the airGR function
  InputsModel <- CreateInputsModel(
    FUN_MOD,
-    DatesR = gits$date,
-    Precip = gits[[id]]$Precip,
-    PotEvap = gits[[id]]$PotEvap,
+    DatesR = DatesR,
+    Precip = Precip,
+    PotEvap = PotEvap,
    Qupstream = Qupstream,
    LengthHydro = LengthHydro,
    BasinAreas = BasinAreas

--- a/R/CreateInputsModel.default.R
+++ b/R/CreateInputsModel.default.R
-#' Wrapper for the airGR::CreateInputsModel function
+#' Wrapper for \code{\link[airGR]{CreateInputsModel}} for one sub-basin.
 #'
-#' @param x hydrological model function (e.g. \code{\link[airGR]{RunModel_GR4J}}, \code{\link[airGR]{RunModel_CemaNeigeGR4J}})
-#' @param ... further arguments passed to \code{\link[airGR]{CreateInputsModel}}.
-#'
-#' @return object of class \emph{InputsModel}, see \code{\link[airGR]{CreateInputsModel}} for details.
+#' @inherit airGR::CreateInputsModel
 #' @import airGR
 #' @export
-#' @seealso The original function in airGR package: \code{\link[airGR]{CreateInputsModel}}.
 #'
 CreateInputsModel.default <- function(x,
                                      ...) {

--- a/R/CreateRunOptions.InputsModel.R
+++ b/R/CreateRunOptions.InputsModel.R
-#' Create \emph{RunOptions} object for airGR. See \code{\link[airGR]{CreateOptions}}.
+#' Wrapper for \code{\link[airGR]{CreateRunOptions}} for one sub-basin.
 #'
-#' @param InputsModel object of class \emph{InputsModel}, see \code{\link[airGR]{CreateInputsModel}} for details.
-#' @param ... further arguments passed to \code{\link[airGR]{CreateOptions}}.
-#'
-#' @return See \code{\link[airGR]{CreateOptions}}.
+#' @inherit airGR::CreateRunOptions
 #' @export
 CreateRunOptions.InputsModel <- function(InputsModel, ...) {


--- a/R/ginet.R
+++ b/R/ginet.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", runoff = "runoff"), keep_all = FALSE) {
-  colsDefault <- list(id = "id", down = "down", length = "length", runoff = "runoff")
+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)

--- a/R/RunModel.GriwrmInputsModel.R
+++ b/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]]
    )

  }

--- a/R/RunModel.InputsModel.R
+++ b/R/RunModel.InputsModel.R
-#' Wrapper for \code{\link[airGR]{RunModel}} which performs a single model run with the provided function over the selected period.
+#' Wrapper for \code{\link[airGR]{RunModel}} for one sub-basin.
 #'
-#' @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
+#' @inherit airGR::RunModel
 #' @export
 RunModel.InputsModel <- function(InputsModel, RunOptions, Param, FUN_MOD = NULL, ...) {
  if(is.null(FUN_MOD)) {

--- a/R/girop.R
+++ b/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
-}
--- a/R/gits.R
+++ b/R/gits.R
-#' Title
-#'
-#' @param id string of the id of the node
-#' @param ts numeric matrix or data frame containing 3 columns for precipitation, evaporation, and observed flow
-#' @param cols named list or vector used for matching the columns of ts with the required columns names which are "Precip", "PotEvap", and "Qobs".
-#'
-#' @return \emph{Gits} class object which is a list containing a `date` element (Vector of PosiXlt timestamps) and an element named the id of the node containing a dataframe with observed data.
-#' @export
-Gits <- function(id, ts,
-                 cols = list(date = "date", Precip = "Precip", PotEvap = "PotEvap", Qobs = "Qobs")) {
-
-  cols <- as.list(cols)
-  ts <- dplyr::rename(ts, unlist(cols))
-
-  if(any(is.na(ts$Qobs))) {
-    stop("Qobs should not contain any NA")
-  }
-  if(any(ts$Qobs < 0)) {
-    stop("Qobs should be strictly positive")
-  }
-
-  gitsOut <- list(date = ts$date)
-  cols$date <- NULL
-  gitsOut[[id]] <- dplyr::select(ts, names(cols))
-  class(gitsOut) <- append(class(gitsOut), "Gits")
-  gitsOut
-}
-
-#' Merge two gits objects with identical date time series.
-#'
-#' @param x Gits object to merge (See [Gits]).
-#' @param y Gits object to merge (See [Gits]).
-#' @param ... For merge generic function compatibility.
-#'
-#' @return Gits object merged with one item `Date` and Items corresponding to each node.
-#' @export
-merge.Gits <- function(x, y, ...) {
-  if(!is(y, "Gits")) {
-    stop("A Gits class object can only be merged with a Gits class object")
-  }
-  if(! identical(x$date, y$date)) {
-    stop("Time series dates are not identical")
-  }
-  y$date <- NULL
-  x <- utils::modifyList(x, y)
-}
--- a/inst/seine_data/network_gauging_stations.txt
+++ b/inst/seine_data/network_gauging_stations.txt
+id_sgl	id_hydro	lambert2.x	lambert2.y	area	description	id_aval	distance_aval
+TRANN_01		766626.06	2369152.25	1557.06	l'Aube à Trannes	ARCIS_24	68100
+GURGY_02	H2221010	689713.00	2320549.00	3819.77	L'Yonne à Gurgy	COURL_23	83612
+BRIEN_03	H2482010	695313.00	2332549.00	2979.77	L'Armançon à Brienon-sur-Armançon	COURL_23	84653
+STDIZ_04	H5071010	791113.00	2407349.00	2347.53	La Marne à Saint-Dizier	CHALO_21	85570
+PARIS_05	H5920010	602213.00	2427449.00	43824.66	La Seine à Paris
+BAR-S_06	H0400010	751913.00	2348349.00	2340.37	La Seine à Bar-sur-Seine	MERY-_22	79766
+CHAUM_07		716518.38	2241747.00	216.50	L'Yonne à Chaumard	GURGY_02	153074
+CUSSY_08	H2172310	726013.00	2275149.00	247.99	Le Cousin à Cussy-les-Forges	GURGY_02	91378
+STGER_09		718512.88	2266649.25	402.74	La Cure à St-Germain	GURGY_02	94152
+GUILL_10	H2322020	731013.00	2282349.00	488.71	Le Serein à Guillon	CHABL_12	66026
+AISY-_11	H2452020	742413.00	2298149.00	1349.51	L'Armançon à Aisy-sur-Armançon	BRIEN_03	102428
+CHABL_12	H2342010	709613.00	2314149.00	1116.27	Le Serein à Chablis	COURL_23	111781
+NOGEN_13		685912.88	2389349.25	9182.39	La Seine à Nogent-sur-Seine	MONTE_15	63215
+EPISY_14	H3621010	633413.00	2371049.00	3916.71	Le Loing à Épisy	ALFOR_16	89196
+MONTE_15		645112.88	2376849.25	21199.39	La Seine à Montereau	ALFOR_16	94475
+ALFOR_16	H4340020	606013.00	2420349.00	30784.71	La Seine à Alfortville	PARIS_05	9263
+NOISI_17	H5841010	620913.00	2428949.00	12547.72	La Marne à Noisiel	PARIS_05	39384
+MONTR_18	H5752020	638013.00	2431849.00	1184.81	Le Grand Morin à Montry	NOISI_17	37915
+LOUVE_19	H5083050	791613.00	2393949.00	461.74	La Blaise à Louvemont	CHALO_21	86165
+LASSI_20	H1362010	759513.00	2385549.00	876.53	La Voire à Lassicourt	ARCIS_24	43618
+CHALO_21	H5201010	747713.00	2441349.00	6291.55	La Marne à Châlons-sur-Marne	NOISI_17	237937
+MERY-_22	H0810010	714913.00	2390949.00	3899.62	La Seine à Méry-sur-Seine	NOGEN_13	49933
+COURL_23	H2721010	660813.00	2370449.00	10687.35	L'Yonne à Courlon-sur-Yonne	MONTE_15	26159
+ARCIS_24	H1501010	733313.00	2394749.00	3594.60	L'Aube à Arcis-sur-Aube	NOGEN_13	70926
+VITRY_25	H5172010	768513.00	2418849.00	2109.14	La Saulx à Vitry-en-Perthois	CHALO_21	38047
--- a/vignettes/V01_First_network.Rmd
+++ b/vignettes/V01_First_network.Rmd
@@ -22,106 +22,86 @@ List of nodes

 ```{r}
 seine_nodes <- readr::read_delim(
-  file = "https://stratus.irstea.fr/d/0b18e688851a45478f7a/files/?p=/climaware_hydro/griwrm_network.txt&dl=1", 
-  delim = ";"
+  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 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.
+`Griwrm` 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$distance_aval / 1000
-# Generate the ginet object 
-ginet <- Ginet(seine_nodes, list(id = "id_sgl", down = "id_aval"))
-ginet
+seine_nodes$model <- "RunModel_GR4J"
+# Generate the griwrm object
+griwrm <- Griwrm(seine_nodes, list(id = "id_sgl", down = "id_aval", length = "distance_aval"))
+griwrm
 ```

-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:
+## Observation time series

- `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
+Loading hydrometeorological data on the Seine river basin from the ClimAware project:

-```{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 
+```{r, warning=FALSE, message=FALSE}

-Loading hydrometeorological data on the Seine river basin from the ClimAware project: 
+Precip <- NULL
+PotEvap <- NULL
+Qobs <- NULL

-```{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
-
-load_ts <- function(x) {
-  ts <- readr::read_delim(file = x, 
-             delim = ";", skip = 16, trim_ws = TRUE)
-  ts$Date <- as.POSIXlt(lubridate::ymd(ts$Date))
-  # Interpolation of data gap in the discharge time serie
-  ts[ts$Qnat < 0, "Qnat"] <- NA
-  if(is.na(ts$Qnat[nrow(ts)])) {
-    ts$Qnat[nrow(ts)] <- 0 # No value at the end: time serie converge to zero
+MergeTS <- function(dfOld, id, dfNew) {
+    names(dfNew) <- c("DatesR", id) # Renaming columns of the new input into date and sub-basin ID
+    if(is.null(dfOld)) {
+    dfOut <- dfNew # Creation of the first column
+  } else {
+    dfOut <- merge(dfOld, dfNew, by = "DatesR", all = TRUE) # Merge the new columns respecting to date column
  }
-  ts$Qnat <- zoo::na.approx(ts$Qnat)
-  ts
+  return(dfOut)
 }

-l <- lapply(urls, load_ts)
-
-```
-
-`Gits` object is a list containing a item named `date` with a timestamp vector of the time series and items named by the identifier of each node. These items contain a dataframe with the observations.
-
-The Gits function creates a `Gits` object 
-
-```{r}
-gits <- Gits(ginet$id[1], l[[ginet$id[1]]], cols = list(date = "Date", Precip = "Ptot", PotEvap = "ETP", Qobs = "Qnat"))
-```
-
-Copy the observations for each node the ginet network:
-
-```{r}
-for(id in ginet$id) {
-  l[[id]]$Qnat
-  l[[id]]$Qnat <- l[[id]]$Qnat * 86.4 / girop$area[girop$id == id]
-  l[[id]]$Qnat[l[[id]]$Qnat < 0] <- NA
-  gits <- merge(gits, Gits(id, l[[id]], cols = list(date = "Date", Precip = "Ptot", PotEvap = "ETP", Qobs = "Qnat")))
+for(id in griwrm$id) {
+  url <-
+    file.path(
+      "https://stratus.irstea.fr/d/0b18e688851a45478f7a/files/?p=/climaware_hydro/Q_OBS_NAT",
+      paste0(id, "_NAT.txt&dl=1")
+    )
+  ts <- readr::read_delim(file = url,
+                          delim = ";", skip = 16, trim_ws = TRUE)
+  # Date conversion to POSIX
+  ts$Date <- as.POSIXlt(lubridate::ymd(ts$Date))
+  # Ptot column  is merged into Precip dataframe
+  Precip <- MergeTS(Precip, id, ts[,c("Date", "Ptot")])
+  # ETP column is merged into PotEvap dataframe
+  PotEvap <- MergeTS(PotEvap, id, ts[,c("Date", "ETP")])
+  # Convert Qobs from m3/s to mm/time step
+  ts$Qnat <- ts$Qnat * 86.4 / griwrm$area[griwrm$id == id]
+  # Setting data gaps to NA
+  ts$Qnat[ts$Qnat <= 0] <- NA
+  # Qnat column is merged into Qobs dataframe
+  Qobs <- MergeTS(Qobs, id, ts[,c("Date", "Qnat")])
 }
+DatesR <- Precip$DatesR
+Precip$DateR <- NULL
+PotEvap$DateR <- NULL
+Qobs$DateR <- NULL
 ```

 ## Generate the GRIWRM InputsModel object

 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, girop, gits)
+InputsModel <- CreateInputsModel(griwrm, DatesR, Precip, PotEvap, Qobs)
 ```


@@ -129,7 +109,8 @@ InputsModel <- CreateInputsModel(ginet, girop, gits)
 ## Save data for next vignettes

 ```{r}
+
 dir.create("_cache", showWarnings = FALSE)
-save(ginet, girop, gits, InputsModel, file = "_cache/V01.RData")
+save(griwrm, Qobs, InputsModel, file = "_cache/V01.RData")
 ```

--- a/vignettes/V03_First_Calibration.Rmd
+++ b/vignettes/V03_First_Calibration.Rmd
@@ -25,9 +25,9 @@ load("_cache/V02.RData")

 ```{r}
 InputsCrit <- CreateInputsCrit(
-  InputsModel = InputsModel, 
+  InputsModel = InputsModel,
  FUN_CRIT = airGR::ErrorCrit_KGE2,
-  RunOptions = RunOptions, gits = gits
+  RunOptions = RunOptions, Qobs = Qobs
 )
 str(InputsCrit)
 ```
@@ -53,25 +53,29 @@ 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(griwrm$id, function(x) {OutputsCalib[[x]]$Param})

 OutputsModels <- RunModel(
  InputsModel = InputsModel,
  RunOptions = RunOptions,
-  girop = giropMichel
+  Param = ParamMichel
 )
 ```

+## Save calibration data for next vignettes
+
+```{r}
+save(ParamMichel, file = "_cache/V03.RData")
+```
+
+
 ## Plot the result for each basin

 ```{r, fig.height = 5, fig.width = 8}
 htmltools::tagList(lapply(
-  names(OutputsModels), 
+  names(OutputsModels),
  function(x) {
-    plot(OutputsModels[[x]], Qobs = gits[[x]]$Qobs[RunOptions[[x]]$IndPeriod_Run] , main = x)
+    plot(OutputsModels[[x]], Qobs = Qobs[RunOptions[[x]]$IndPeriod_Run,x] , main = x)
  }
 ))
 ```