.gitlab-ci.yml

 stages:
-    - update_packages
-    - build
     - checks
 
 default:
@@ -8,40 +6,36 @@ default:
 
 image: r-base:latest
 
+variables:
+  R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib"
+  CHECK_DIR: "$CI_PROJECT_DIR/ci/logs"
+  BUILD_LOGS_DIR: "$CI_PROJECT_DIR/ci/logs/$CI_PROJECT_NAME.Rcheck"
+
 cache:
   paths:
-    - R_LIBS/
+    - $R_LIBS_USER
 
 before_script:
-  - echo "R_LIBS='$(pwd)/R_LIBS'" > .Renviron
-
-update_packages:
-  stage: update_packages
-  script:
-    - mkdir -p R_LIBS
-    - Rscript -e 'if(!dir.exists("R_LIBS/remotes")) install.packages("remotes", lib = "R_LIBS")'
-    - apt-get update && apt-get -y install libxml2-dev
-    - Rscript -e 'remotes::update_packages(c("dplyr", "rmarkdown", "readr", "lubridate", "zoo", "roxygen2", "DiagrammeR"), lib = "R_LIBS")'
-    - Rscript -e 'remotes::install_gitlab("HYCAR-Hydro/airgr@sd", host = "gitlab.irstea.fr", lib = "R_LIBS")'
-
-build:
-  stage: build
+  - apt-get update && apt-get -y install libcurl4-openssl-dev libxml2-dev libssl-dev
+  - mkdir -p $R_LIBS_USER $BUILD_LOGS_DIR
+  - echo "R_LIBS='$R_LIBS_USER'" > .Renviron
+  - R -e 'if(!dir.exists(file.path(Sys.getenv("R_LIBS_USER"), "devtools"))) install.packages("devtools")'
+  - R -e 'remotes::install_gitlab("HYCAR-Hydro/airgr@dev", host = "gitlab.irstea.fr")'
+  - R -e 'devtools::install_deps(dep = T)'
+  - R -e "devtools::document(roclets = c('rd', 'collate', 'namespace'))"
+
+.check:
+  stage: checks
   script:
-    - apt-get update && apt-get -y install libxml2-dev
-    - Rscript -e "roxygen2::roxygenise()"
-    - R CMD build ../griwrm
-  artifacts:
-    paths:
-      - griwrm_*.tar.gz
+    - R -e 'devtools::check(check_dir = Sys.getenv("CHECK_DIR"), cran = !as.logical(Sys.getenv("NOT_CRAN")))'
+    - R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
 
 check_not_cran:
-  stage: checks
   variables:
     NOT_CRAN: "true"
-  script:
-    - R CMD check --no-manual griwrm_*.tar.gz
+  extends: .check
 
 check_as_cran:
-  stage: checks
-  script:
-    - R CMD check --as-cran --no-manual griwrm_*.tar.gz
+  variables:
+    NOT_CRAN: "false"
+  extends: .check

DESCRIPTION

 Package: airGRiwrm
 Title: airGR Integrated Water Resource Management
-Version: 0.3.1
-Authors@R:
-    person(given = "David",
-           family = "Dorchies",
-           role = c("aut", "cre"),
-           email = "david.dorchies@inrae.fr",
-           comment = c(ORCID = "0000-0002-6595-7984"))
-Description: This R package aims to model water basin using airGR based semi-distributive model with the integration of human infrastructures and their management.
+Version: 0.3.4
+Authors@R: c(
+    person("David", "Dorchies", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6595-7984"), email = "david.dorchies@inrae.fr"),
+    person("Olivier", "Delaigue", role = c("ctb"), comment = c(ORCID = "0000-0002-7668-8468"), email = "airGR@inrae.fr"),
+    person("Guillaume", "Thirel", role = c("ctb"), comment = c(ORCID = "0000-0002-1444-1830"))
+    )
+Description: This R package aims to model water basin using 'airGR' based semi-distributive model with the integration of human infrastructures and their management.
 License: AGPL-3
 Encoding: UTF-8
 LazyData: true
@@ -16,8 +15,7 @@ RoxygenNote: 7.1.1
 Imports:
     dplyr,
     utils,
-    airGR (>= 1.6.1.11),
-    methods
+    airGR (>= 1.6.1.11)
 Suggests:
     knitr,
     rmarkdown,

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}}.

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.

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.
+#' @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}}.
 #'

R/CreateInputsCrit.R

 #' Title
 #'
-#' @param InputsModel InputsModel for GR-IWRM (See \code{[CreateInputsModel.Griwrm]}) or AirGR (See \code{\link[airGR]{CreateInputsModel}})
+#' @param InputsModel InputsModel for GR-IWRM (See \code{[CreateInputsModel.GRiwrm]}) or AirGR (See \code{\link[airGR]{CreateInputsModel}})
 #' @param ... further arguments passed to or from other methods.
 #'
 #' @return

R/CreateInputsModel.Griwrm.R

 #' Create InputsModel object for a GRIWRM network
 #'
-#' @param x Griwrm object describing the diagram of the semi-distributed model, see \code{[Griwrm]}.
-#' @param DateR Vector of POSIXlt observation time steps.
+#' @param x GRiwrm object describing the diagram of the semi-distributed model, see \code{[GRiwrm]}.
+#' @param DatesR Vector of POSIXt 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.
@@ -10,7 +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, 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
@@ -38,7 +38,7 @@ CreateEmptyGriwrmInputsModel <- function() {
 #' Create one InputsModel for a GRIWRM node
 #'
 #' @param id string of the node identifier
-#' @param griwrm See \code{[Griwrm]}.
+#' @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).

R/CreateRunOptions.GriwrmInputsModel.R

 #' 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.

R/CreateRunOptions.R

 #' 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

-#' Display a diagram representing the network structure of a Griwrm object
+#' Display a diagram representing the network structure of a GRiwrm object
 #'
-#' @param griwrm the Griwrm object to display.
+#' @param griwrm the GRiwrm object to display.
 #' @param display if `TRUE` displays the diagram with `DiagrammeR::mermaid`, return the mermaid code otherwise.
 #' @param orientation Orientation of the graph. "LR" by default.
 #'

R/Griwrm.R

@@ -5,28 +5,28 @@
 #' @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 `Griwrm` 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
-Griwrm <- 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", "Griwrm"))
+  class(db) <- append(class(db), c("GRiwrm", "GRiwrm"))
   db
 }
 
 #' Sort the nodes from upstream to downstream.
 #'
-#' @param griwrm See \code{[Griwrm]}.
+#' @param griwrm See \code{[GRiwrm]}.
 #'
 #' @return vector with the ordered node names.
 #' @export
 getNodeRanking <- function(griwrm) {
-  if(!is(griwrm, "Griwrm")) {
-    stop("getNodeRanking: griwrm argument should be of class Griwrm")
+  if(!inherits(griwrm, "GRiwrm")) {
+    stop("getNodeRanking: griwrm argument should be of class GRiwrm")
   }
   # Remove nodes without model (direct flow connections treated as upstream flows only)
   griwrm <- griwrm[!is.na(griwrm$model),]

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.

R/UpdateQsimUpstream.R

 #' 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]}.
 #'

README.md

-# airGR-IWRM: airGR based Integrated Water Resource Management R package
+# airGRiwrm: airGR based Integrated Water Resource Management R package
 
-airGR-IWRM is an extension of the airGR R package for managing semi-distributive hydrological model on an anthropized catchment.
+airGRiwrm is an extension of the airGR R package for managing semi-distributive hydrological model on an anthropized catchment.
 
 This package is developed as part of the IN-WOP project (http://www.waterjpi.eu/joint-calls/joint-call-2018-waterworks-2017/booklet/in-wop) by the mixed research unit G-EAU (https://g-eau.fr).
 
@@ -11,7 +11,7 @@ This package is developed as part of the IN-WOP project (http://www.waterjpi.eu/
 This package depends on airGR version 1.6. or more which is currently under development. To install it, use the following instruction:
 
 ```
-remotes::install_gitlab("HYCAR-Hydro/airgr@sd", host = "gitlab.irstea.fr")
+remotes::install_gitlab("HYCAR-Hydro/airgr@dev", host = "gitlab.irstea.fr")
 ```
 
 ### Local installation

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
+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

inst/seine_data/network_reservoir_connections.txt

-id	length	down
-AUBE-_P2	66500	ARCIS_24
-AUBE-_R3	44500	ARCIS_24
-MARNE_P23	3000	STDIZ_04
-MARNE_P28	82420	CHALO_21
-MARNE_R25	56870	CHALO_21
-PANNEC_P	153074	GURGY_02
-PANNEC_R	153074	GURGY_02
-SEINE_P7	73766	MERY-_22
-SEINE_R8	41766	MERY-_22
+id;length;down
+AUBE-_P2;66500;ARCIS_24
+AUBE-_R3;44500;ARCIS_24
+MARNE_P23;3000;STDIZ_04
+MARNE_P28;82420;CHALO_21
+MARNE_R25;56870;CHALO_21
+PANNEC_P;153074;GURGY_02
+PANNEC_R;153074;GURGY_02
+SEINE_P7;73766;MERY-_22
+SEINE_R8;41766;MERY-_22

vignettes/V01_First_network.Rmd

@@ -21,14 +21,14 @@ library(airGRiwrm)
 List of nodes
 
 ```{r}
-seine_nodes <- readr::read_delim(
+seine_nodes <- read.table(
   file = system.file("seine_data", "network_gauging_stations.txt", package = "airGRiwrm"),
-  delim = "\t"
+  sep = ";", header = TRUE, fileEncoding = "UTF-8", quote = "\""
 )
 seine_nodes
 ```
 
-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:
+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.
@@ -36,12 +36,12 @@ Create the Griwrm 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.
 
-`Griwrm` 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 Griwrm object
-griwrm <- Griwrm(seine_nodes, list(id = "id_sgl", down = "id_aval", length = "distance_aval"))
+# Generate the GRiwrm object
+griwrm <- GRiwrm(seine_nodes, list(id = "id_sgl", down = "id_aval", length = "distance_aval"))
 griwrm
 ```
 
@@ -79,10 +79,9 @@ for(id in griwrm$id) {
       "https://stratus.irstea.fr/d/0b18e688851a45478f7a/files/?p=/climaware_hydro/Q_OBS_NAT",
       paste0(id, "_NAT.txt&dl=1")
     )
-  ts <- readr::read_delim(file = url,
-                          delim = ";", skip = 16, trim_ws = TRUE)
+  ts <- read.table(url, sep = ";", skip = 16, header = TRUE)
   # Date conversion to POSIX
-  ts$Date <- as.POSIXlt(lubridate::ymd(ts$Date))
+  ts$Date <- as.POSIXct(as.character(ts$Date), format = "%Y%m%d")
   # Ptot column  is merged into Precip dataframe
   Precip <- MergeTS(Precip, id, ts[,c("Date", "Ptot")])
   # ETP column is merged into PotEvap dataframe
@@ -95,9 +94,9 @@ for(id in griwrm$id) {
   Qobs <- MergeTS(Qobs, id, ts[,c("Date", "Qnat")])
 }
 DatesR <- Precip$DatesR
-Precip$DateR <- NULL
-PotEvap$DateR <- NULL
-Qobs$DateR <- NULL
+Precip$DatesR <- NULL
+PotEvap$DatesR <- NULL
+Qobs$DatesR <- NULL
 ```
 
 ## Generate the GRIWRM InputsModel object

vignettes/V02_First_run.Rmd

@@ -15,7 +15,6 @@ knitr::opts_chunk$set(echo = TRUE)
 
 ```{r}
 library(airGRiwrm)
-library(lubridate)
 ```
 
 
@@ -34,7 +33,7 @@ load("_cache/V01.RData")
 Data comes from calibration of ClimAware project with naturalised flows.
 
 ```{r}
-ClimAwareParams <- readr::read_csv(
+ClimAwareParams <- read.csv(
   file = "https://stratus.irstea.fr/d/0b18e688851a45478f7a/files/?p=/climaware_hydro/Ident_NAT_P0P0.txt&dl=1"
 )
 
@@ -80,7 +79,7 @@ The user must at least define the following arguments:
 
 ```{r}
 IndPeriod_Run <- seq(
-  which(InputsModel[[1]]$DatesR == (InputsModel[[1]]$DatesR[1] %m+% years(1))), # Set aside warm-up period
+  which(InputsModel[[1]]$DatesR == (InputsModel[[1]]$DatesR[1] + 365*24*60*60)), # Set aside warm-up period
   length(InputsModel[[1]]$DatesR) # Until the end of the time series
 )
 ```

vignettes/V04_Open-loop_influenced_flow.Rmd

@@ -164,14 +164,14 @@ style MARNE_R25 fill:#fcc
 Hence the topological connection to the reservoirs is described in the model as below:
 
 ```{r}
-reservoir_connections <- readr::read_delim(
+reservoir_connections <- read.table(
   file = system.file("seine_data", "network_reservoir_connections.txt", package = "airGRiwrm"),
-  delim = "\t"
+  sep = ";", header = TRUE
 )
 reservoir_connections
 ```
 
-Reservoir connections are added to the Griwrm object:
+Reservoir connections are added to the GRiwrm object:
 
 ```{r}
 reservoir_connections$model <- NA
@@ -196,18 +196,14 @@ Then, we load observation data for each reservoir and each connection:
 ```{r}
 
 for(reservoir_id in names(lCfgReservoirs)) {
-  df <- readr::read_delim(
+  df <- read.table(
     file = file.path(
       "https://stratus.irstea.fr/d/0b18e688851a45478f7a/files/?p=/Reservoir_current_rules",
       paste0(lCfgReservoirs[[reservoir_id]]$file, "&dl=1")
     ),
-    delim = "\t",
-    col_types = readr::cols(
-      Date = readr::col_character(),
-      .default = readr::col_double()
-    )
+    sep = "\t", header = TRUE, fill = TRUE
   )
-  df$Date <- format(as.POSIXlt(lubridate::dmy(df$Date)), "%Y-%m-%d")
+  df$Date <- format(as.POSIXct(df$Date))
   Qreservoir <- merge(data.frame(Date = format(DatesR, "%Y-%m-%d")), df, by = "Date", all.x = TRUE)
   for(connect in names(lCfgReservoirs[[reservoir_id]]$connections)) {
     # Replace data gap by zeros (should be interpolated ?)
@@ -224,7 +220,7 @@ for(reservoir_id in names(lCfgReservoirs)) {
   }
 }
 # Convert flows from m3/s to m3/day
-Qobs[,-1] <- Qobs[,-1] * 86400
+Qobs <- Qobs * 86400
 
 ```
 
@@ -298,10 +294,10 @@ for(id in ids) {
       "https://stratus.irstea.fr/d/0b18e688851a45478f7a/files/?p=/climaware_hydro/Q_OBS_NAT",
       paste0(id, "_BV.txt&dl=1")
     )
-  ts <- readr::read_delim(file = url,
-                          delim = ";", skip = 24, trim_ws = TRUE)
+  ts <- read.table(file = url,
+                   sep = ";", skip = 24, header = TRUE)
   # Date conversion to POSIX
-  ts$Date <- as.POSIXlt(lubridate::ymd(ts$Date))
+  ts$Date <- as.POSIXct(as.character(ts$Date), format = "%Y%m%d")
     # Convert Qobs from l/s to mm/time step
   ts$Q <- ts$Q * 86.4 / griwrm$area[griwrm$id == id] / 1000
   # Setting data gaps to NA
@@ -321,7 +317,7 @@ ReduceOutputsModel <- function(OutputsModels, IndPeriod) {
   return(OutputsModelsOut)
 }
 
-QobsReservoirs <- Qobs[Qobs$DatesR < "2008-08-01",c("DatesR", reservoir_connections$id)]
+QobsReservoirs <- Qobs[DatesR < "2008-08-01", reservoir_connections$id]
 save(QobsReservoirs, Qobs2, griwrm2, ReduceOutputsModel, file = "_cache/V04.RData")
 ```
 

vignettes/V05_Open-loop_influenced_flow_calibration.Rmd

@@ -43,7 +43,7 @@ Generate `GriwrmInputsModel` object
 
 ```{r}
 Qobs3 <- cbind(Qobs2, QobsReservoirs)
-iEnd <-which(DatesR == lubridate::ymd("2008-07-31"))
+iEnd <-which(DatesR == as.POSIXct("2008-07-31"))
 InputsModel3 <- CreateInputsModel(griwrm3, DatesR[1:iEnd], Precip[1:iEnd,], PotEvap[1:iEnd,], Qobs3)
 ```
 
@@ -52,7 +52,7 @@ InputsModel3 <- CreateInputsModel(griwrm3, DatesR[1:iEnd], Precip[1:iEnd,], PotE
 
 ```{r}
 IndPeriod_Run <- seq(
-  which(InputsModel3[[1]]$DatesR == (InputsModel3[[1]]$DatesR[1] + months(12))), # Set aside warm-up period
+  which(InputsModel3[[1]]$DatesR == (InputsModel3[[1]]$DatesR[1] + 365*24*60*60)), # Set aside warm-up period
   length(InputsModel3[[1]]$DatesR) # Until the end of the time series
 )
 ```