.Rbuildignore

 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.Rprofile$
+^packrat/
+^tests/tmp/
+^\.gitlab-ci.yml$
+^\.regressionignore$
+^\.vignettechunkignore$
+^\.gitlab-ci\.yml$
+^\.vscode$
+^Rplots\.pdf$
+^ci$
+^data-raw$
+^revdep$
+^\.devcontainer$

.devcontainer/devcontainer.json

+{
+	"image": "rocker/geospatial:devel",
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"eamodio.gitlens",
+				"REditorSupport.r"
+			]
+		}
+	},
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "R -q -e 'install.packages(\"languageserver\");remotes::install_deps(dep = TRUE)'",
+	"postStartCommand": "R -q -e 'devtools::install()'"
+}

.gitignore

-.Rproj.user
+# Specific files for airGR
+packrat/lib*/
+
+# Compiled files
+/src/*.o
+/src/*.so
+/src/*.dll
+/src-*
+
+# Test temporary files
+/tests/tmp/
+*.pdf
+!man/figures/*.pdf
+
+# revdep
+/revdep/
+
+######################################################################################################
+### Generic .gitignore for R (source: https://github.com/github/gitignore/blob/master/R.gitignore) ###
+######################################################################################################
+
+# History files
 .Rhistory
+.Rapp.history
+
+# Session Data files
 .RData
-airGR.Rproj
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+.Rprofile
+
+# pkgdown site
+docs/
+
+# vscode IDE
+.vscode/*
+*.code-workspace
+.history/

.gitlab-ci.yml

+stages:
+  - check
+  - scheduled_tests
+  - revdepcheck
+
+variables:
+  R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib"
+
+default:
+  tags: [docker]
+
+cache:
+  key: "airGR-${R_VERSION}"
+  paths:
+    - $R_LIBS_USER
+
+before_script:
+  - mkdir -p $R_LIBS_USER
+  - echo "R_LIBS='$R_LIBS_USER'" > .Renviron
+  - echo 'options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/focal/latest"))' > .Rprofile
+  - apt-get update && apt-get install -y libstdc++6
+  - R -q -e 'remotes::install_deps(dependencies = TRUE)'
+
+.R-devel:
+  image: rocker/geospatial:devel
+  variables:
+    R_VERSION: devel
+
+.R-patched:
+  only:
+    refs:
+      - tags
+      - schedules
+  image: rocker/geospatial:latest
+  variables:
+    R_VERSION: patched
+
+.R-oldrel:
+  only:
+    refs:
+      - tags
+      - schedules
+  image: rocker/geospatial:4.1
+  variables:
+    R_VERSION: oldrel
+
+.scheduled_tests:
+  only:
+    refs:
+      - tags
+      - schedules
+      - master
+  stage: scheduled_tests
+  script:
+    - R -q -e 'devtools::install()'
+    - Rscript tests/scheduled_tests/scheduled.R
+    - Rscript tests/scheduled_tests/regression.R stable
+    - R CMD INSTALL .
+    - Rscript tests/scheduled_tests/regression.R dev
+    - Rscript tests/scheduled_tests/regression.R compare
+
+.check:
+  stage: check
+  script:
+  - R -q -e 'tinytex::tlmgr("option repository https://ftp.tu-chemnitz.de/pub/tug/historic/systems/texlive/2021/tlnet-final")'
+  - tlmgr update --self && tlmgr install ec epstopdf-pkg amsmath
+  - R -q -e 'remotes::update_packages("rcmdcheck")'
+  - R -q -e 'rcmdcheck::rcmdcheck(args = c("--as-cran"), error_on = "warning")'
+
+.test_all:
+  stage: check
+  script:
+  - R -q -e 'testthat::test_local()'
+
+benchmark_devel:
+  extends: .R-devel
+  stage: check
+  allow_failure: true
+  script:
+  - R -q -e 'remotes::update_packages("microbenchmark", repos = "http://cran.r-project.org")'
+  - R -q -e 'install.packages("airGR", repos = "http://cran.r-project.org")'
+  - Rscript tests/scheduled_tests/benchmarkRunModel.R
+  - R CMD INSTALL .
+  - Rscript tests/scheduled_tests/benchmarkRunModel.R
+  artifacts:
+    paths:
+      - tests/tmp/benchmark.tsv
+      - tests/tmp/mean_execution_time.tsv
+
+scheduled_tests_patched:
+  extends:
+    - .scheduled_tests
+    - .R-patched
+
+scheduled_tests_devel:
+  extends:
+    - .scheduled_tests
+    - .R-devel
+
+scheduled_tests_oldrel:
+  extends:
+    - .scheduled_tests
+    - .R-oldrel
+
+check_patched:
+  extends:
+    - .check
+    - .R-patched
+
+check_devel:
+  extends:
+    - .check
+    - .R-devel
+
+test_all_patched:
+  extends:
+    - .test_all
+    - .R-patched
+
+test_all_devel:
+  extends:
+    - .test_all
+    - .R-devel
+
+test_all_oldrel:
+  extends:
+    - .test_all
+    - .R-oldrel
+
+revdepcheck_devel:
+  stage: revdepcheck
+  only:
+    refs:
+      - tags
+      - schedule
+      - master
+  extends: .R-devel
+  script:
+    - R -q -e 'remotes::install_github("https://github.com/r-lib/revdepcheck")'
+    - R -q -e 'revdepcheck::revdep_check(timeout = as.difftime(20, units = "mins"))'
+    - R -q -e 'stopifnot(all("+" == sapply(revdepcheck::revdep_summary(), "[[", "status")))'
+    - R -q -e 'if (any(sapply(revdepcheck::revdep_summary(), function(x) {any(x$cmp$change == 1)}))) stop()'
+  artifacts:
+    when: on_failure
+    paths:
+      - revdep/README.md
+      - revdep/problems.md
+      - revdep/failures.md
+      - revdep/cran.md
+      - revdep/checks/*.log

.regressionignore

+# .test-regression.ignore contains the list of topic/variables produces by
+# documentation examples that should be ignore in the regression test
+# The format of this file is: 5 lines of comments followed by one line by
+# ignored variable : [Topic]<SPACE>[Variable] or *<SPACE>[Variable] for every variable whatever the topic
+# Example for ignoring OutputsModel variable produced by example("RunModel_GR2M"): RunModel_GR2M OutputsModel

.vignettechunkignore

+# This file is used by the script tests/testthat/test-vignettes which test all
+# chunks including those with `eval=FALSE`
+# It serves to ignore chunks that should not be tested anyway
+# Format: `vignette file name`[space]`id of the chunk`
+V02.1_param_optim.Rmd hydroPSO1
+V02.1_param_optim.Rmd hydroPSO2
+V02.1_param_optim.Rmd resGLOB

DESCRIPTION

 Package: airGR
 Type: Package
-Title: Suite of GR hydrological models for precipitation-runoff modelling
-Version: 1.0.0
-Date: 2016-04-14
+Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling
+Version: 1.7.6.9000
+Date: 2023-10-25
 Authors@R: c(
-  person("Laurent", "Coron", role = c("aut", "cre", "trl")),
-  person("Charles", "Perrin", role = c("aut", "ths")),
+  person("Laurent", "Coron", role = c("aut", "trl"), comment = c(ORCID = "0000-0002-1503-6204")),
+  person("Olivier", "Delaigue", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7668-8468"), email = "airGR@inrae.fr"),
+  person("Guillaume", "Thirel", role = c("aut", "ths"), comment = c(ORCID = "0000-0002-1444-1830")),
+  person("David", "Dorchies", role = c("aut"), comment = c(ORCID = "0000-0002-6595-7984")),
+  person("Charles", "Perrin", role = c("aut", "ths"), comment = c(ORCID = "0000-0001-8552-1881")),
   person("Claude", "Michel", role = c("aut", "ths")),
-  person("Vazken", "Andréassian", role = c("ctb", "ths")),
-  person("Pierre", "Brigode", role = c("ctb")),
-  person("Olivier", "Delaigue", role = c("ctb")),
+  person("Vazken", "Andréassian", role = c("ctb", "ths"), comment = c(ORCID = "0000-0001-7124-9303")),
+  person("François", "Bourgin", role = c("ctb"), comment = c(ORCID = "0000-0002-2820-7260")),
+  person("Pierre", "Brigode", role = c("ctb"), comment = c(ORCID = "0000-0001-8257-0741")),
   person("Nicolas", "Le Moine", role = c("ctb")),
-  person("Thibaut", "Mathevet", role = c("ctb")),
+  person("Thibaut", "Mathevet", role = c("ctb"), comment = c(ORCID = "0000-0002-4142-4454")),
   person("Safouane", "Mouelhi", role = c("ctb")),
-  person("Ludovic", "Oudin", role = c("ctb")),
+  person("Ludovic", "Oudin", role = c("ctb"), comment = c(ORCID = "0000-0002-3712-0933")),
   person("Raji", "Pushpalatha", role = c("ctb")),
-  person("Guillaume", "Thirel", role = c("ctb")),
   person("Audrey", "Valéry", role = c("ctb"))
   )
-Author: Laurent Coron, Charles Perrin, with contributions
- from Vazken Andréassian, Pierre Brigode, Olivier Delaigue,
- Nicolas Le Moine, Thibaut Mathevet, Safouane Mouelhi,
- Ludovic Oudin, Raji Pushpalatha, Guillaume Thirel, Audrey Valéry.
- Based on earlier work by Claude Michel.
-Maintainer: Laurent Coron, Olivier Delaigue <airGR@irstea.fr>
-Depends: R (>= 3.0.1)
-Description: This package brings into R the hydrological modelling tools developed
-  at Irstea-Antony (HBAN Research Unit, France). The package includes several conceptual
-  rainfall-runoff models (GR4H, GR4J, GR5J, GR6J, GR2M, GR1A), a snowmelt module (Cemaneige)
-  and the associated functions for their calibration and evaluation. Use help(airGR) for package description.
+Depends: R (>= 3.1.0)
+Imports:
+  graphics,
+  grDevices,
+  stats,
+  utils
+Suggests:
+  knitr, markdown, rmarkdown,
+  caRamel, coda, DEoptim, FME, ggmcmc, Rmalschains,
+  GGally, ggplot2,
+  testthat
+Description: Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A) that can be applied either on a lumped or semi-distributed way. A snow accumulation and melt model (CemaNeige) and the associated functions for the calibration and evaluation of models are also included. Use help(airGR) for package description and references.
 License: GPL-2
-URL: http://webgr.irstea.fr/modeles/?lang=en
+URL: https://hydrogr.github.io/airGR/
+BugReports: https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues
 NeedsCompilation: yes
 Encoding: UTF-8
-
+VignetteBuilder: knitr
+RoxygenNote: 7.1.1

NAMESPACE

 #####################################
 ##              Load DLL           ##
 #####################################
-useDynLib(airGR)
+useDynLib(airGR, .registration = TRUE)
+
+
+
+#####################################
+##            S3 methods           ##
+#####################################
+S3method('[', InputsModel)
+#S3method('[', OutputsModel) ### to add in version 2.0
+S3method(plot, OutputsModel)
+S3method(SeriesAggreg, data.frame)
+S3method(SeriesAggreg, list)
+S3method(SeriesAggreg, InputsModel)
+S3method(SeriesAggreg, OutputsModel)
 
 
 
@@ -10,9 +23,11 @@ useDynLib(airGR)
 #####################################
 export(Calibration)
 export(Calibration_Michel)
-export(Calibration_optim)
 export(CreateCalibOptions)
+export(CreateErrorCrit_GAPX)
+export(CreateIniStates)
 export(CreateInputsCrit)
+export(CreateInputsCrit_Lavenne)
 export(CreateInputsModel)
 export(CreateRunOptions)
 export(DataAltiExtrapolation_Valery)
@@ -21,26 +36,44 @@ export(ErrorCrit_KGE)
 export(ErrorCrit_KGE2)
 export(ErrorCrit_NSE)
 export(ErrorCrit_RMSE)
-export(PEdaily_Oudin)
+export(Imax)
+export(PE_Oudin)
+export(plot.OutputsModel) ### to remove from version 2.0
 export(RunModel)
 export(RunModel_CemaNeige)
+export(RunModel_CemaNeigeGR4H)
+export(RunModel_CemaNeigeGR5H)
 export(RunModel_CemaNeigeGR4J)
 export(RunModel_CemaNeigeGR5J)
 export(RunModel_CemaNeigeGR6J)
 export(RunModel_GR1A)
 export(RunModel_GR2M)
 export(RunModel_GR4H)
+export(RunModel_GR5H)
 export(RunModel_GR4J)
 export(RunModel_GR5J)
 export(RunModel_GR6J)
+export(RunModel_Lag)
 export(SeriesAggreg)
 export(TransfoParam)
 export(TransfoParam_CemaNeige)
+export(TransfoParam_CemaNeigeHyst)
 export(TransfoParam_GR1A)
 export(TransfoParam_GR2M)
 export(TransfoParam_GR4H)
+export(TransfoParam_GR5H)
 export(TransfoParam_GR4J)
 export(TransfoParam_GR5J)
 export(TransfoParam_GR6J)
-export(plot_OutputsModel)
+export(TransfoParam_Lag)
+#export(.ErrorCrit)
+#export(.FeatModels)
+
 
+#####################################
+##               Import            ##
+#####################################
+import(stats)
+import(graphics)
+import(grDevices)
+import(utils)

R/BasinData.R

-#' @name BasinInfo
-#' @docType data
-#' @title Data sample: characteristics of a fictional catchment (L0123001, L0123002 or L0123003)
-#' @description
-#' R-object containing the code, station's name, area and hypsometric curve of the catchment.
-#' @encoding UTF-8
-#' @format
-#' List named 'BasinInfo' containing
-#' \itemize{
-#' \item two strings: catchment's code and station's name
-#' \item one float: catchment's area in km2
-#' \item one numeric vector: catchment's hypsometric curve (min, quantiles 01 to 99 and max) in metres
-#' }
-#' @examples 
-#'    require(airGR)
-#'    data(L0123001)
-#'    str(BasinInfo)
-
-NULL
-
-
-#' @name BasinObs
-#' @docType data
-#' @title Data sample: time series of observations of a fictional catchment (L0123001, L0123002 or L0123003)
-#' @description
-#' R-object containing the times series of precipitation, temperature, potential evapotranspiration and discharges. \cr
-#' Times series for L0123001 or L0123002 are at the daily time-step for use with daily models such as GR4J, GR5J, GR6J, CemaNeigeGR4J, CemaNeigeGR5J and CemaNeigeGR6J.
-#' Times series for L0123003 are at the hourly time-step for use with hourly models such as GR4H.
-#' @encoding UTF-8
-#' @format
-#' Data frame named 'BasinObs' containing
-#' \itemize{
-#' \item one POSIXlt vector: time series dates in the POSIXlt format
-#' \item five numeric vectors: time series of catchment average precipitation [mm], catchment average air temperature [degC], catchment average potential evapotranspiration [mm], outlet discharge [l/s], outlet discharge [mm]
-#' }
-#' @examples 
-#'    require(airGR)
-#'    data(L0123001)
-#'    str(BasinObs)
-
-NULL
-

R/Calibration.R

-#*************************************************************************************************
-#' Calibration algorithm which minimises the error criterion using the provided functions. \cr
-#*************************************************************************************************
-#' @title  Calibration algorithm which minimises an error criterion on the model outputs using the provided functions
-#' @author Laurent Coron (June 2014)
-#' @seealso \code{\link{Calibration_Michel}}, \code{\link{Calibration_optim}},
-#'          \code{\link{RunModel}}, \code{\link{ErrorCrit}}, \code{\link{TransfoParam}},
-#'          \code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}}, 
-#'          \code{\link{CreateInputsCrit}}, \code{\link{CreateCalibOptions}}.
-#' @example tests/example_Calibration.R
-#' @export
-#' @encoding UTF-8
-#_FunctionInputs__________________________________________________________________________________
-#' @param  InputsModel         [object of class \emph{InputsModel}] see \code{\link{CreateInputsModel}} for details
-#' @param  RunOptions          [object of class \emph{RunOptions}] see \code{\link{CreateRunOptions}} for details
-#' @param  InputsCrit          [object of class \emph{InputsCrit}] see \code{\link{CreateInputsCrit}} for details
-#' @param  CalibOptions        [object of class \emph{CalibOptions}] see \code{\link{CreateCalibOptions}} for details
-#' @param  FUN_MOD             [function] hydrological model function (e.g. RunModel_GR4J, RunModel_CemaNeigeGR4J)
-#' @param  FUN_CRIT            [function] error criterion function (e.g. ErrorCrit_RMSE, ErrorCrit_NSE)
-#' @param  FUN_CALIB           (optional) [function] calibration algorithm function (e.g. Calibration_Michel, Calibration_optim), default=Calibration_Michel
-#' @param  FUN_TRANSFO         (optional) [function] model parameters transformation function, if the FUN_MOD used is native in the package FUN_TRANSFO is automatically defined
-#' @param  quiet               (optional) [boolean] boolean indicating if the function is run in quiet mode or not, default=FALSE
-#_FunctionOutputs_________________________________________________________________________________
-#' @return  [list] see \code{\link{Calibration_Michel}} or \code{\link{Calibration_optim}} 
-#**************************************************************************************************
-Calibration <- function(InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_CALIB=Calibration_Michel,FUN_TRANSFO=NULL,quiet=FALSE){
-    return( FUN_CALIB(InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_TRANSFO,quiet=quiet) )
+Calibration <- function(InputsModel,
+                        RunOptions,
+                        InputsCrit,
+                        CalibOptions,
+                        FUN_MOD,
+                        FUN_CRIT,                      # deprecated
+                        FUN_CALIB = Calibration_Michel,
+                        FUN_TRANSFO = NULL,
+                        verbose = TRUE,
+                        ...) {
+
+  FUN_MOD   <- match.fun(FUN_MOD)
+
+  if (!missing(FUN_CRIT)) {
+    FUN_CRIT <- match.fun(FUN_CRIT)
+  }
+
+  FUN_CALIB <- match.fun(FUN_CALIB)
+
+  if (!is.null(FUN_TRANSFO)) {
+    FUN_TRANSFO <- match.fun(FUN_TRANSFO)
+  }
+
+  return(FUN_CALIB(InputsModel = InputsModel, RunOptions = RunOptions, InputsCrit = InputsCrit,
+                   CalibOptions = CalibOptions,
+                   FUN_MOD = FUN_MOD, FUN_TRANSFO = FUN_TRANSFO,
+                   verbose = verbose, ...))
 }
 

R/Calibration_optim.R

-#*************************************************************************************************
-#' Calibration algorithm which minimises the error criterion. \cr
-#' \cr
-#' The algorithm is based on the "optim" function from the "stats" R-package 
-#' (using method="L-BFGS-B", i.e. a local optimization quasi-Newton method).
-#'
-#' To optimise the exploration of the parameter space, transformation functions are used to convert
-#' the model parameters. This is done using the TransfoParam functions.
-#*************************************************************************************************
-#' @title  Calibration algorithm which minimises the error criterion using the stats::optim function
-#' @author Laurent Coron (August 2013)
-#' @example tests/example_Calibration_optim.R
-#' @seealso \code{\link{Calibration}}, \code{\link{Calibration_Michel}},
-#'          \code{\link{RunModel_GR4J}}, \code{\link{TransfoParam_GR4J}}, \code{\link{ErrorCrit_RMSE}},
-#'          \code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}}, 
-#'          \code{\link{CreateInputsCrit}}, \code{\link{CreateCalibOptions}}.
-#' @encoding UTF-8
-#' @export
-#_FunctionInputs__________________________________________________________________________________
-#' @param  InputsModel         [object of class \emph{InputsModel}] see \code{\link{CreateInputsModel}} for details
-#' @param  RunOptions          [object of class \emph{RunOptions}] see \code{\link{CreateRunOptions}} for details
-#' @param  InputsCrit          [object of class \emph{InputsCrit}] see \code{\link{CreateInputsCrit}} for details
-#' @param  CalibOptions        [object of class \emph{CalibOptions}] see \code{\link{CreateCalibOptions}} for details
-#' @param  FUN_MOD             [function] hydrological model function (e.g. RunModel_GR4J, RunModel_CemaNeigeGR4J)
-#' @param  FUN_CRIT            [function] error criterion function (e.g. ErrorCrit_RMSE, ErrorCrit_NSE)
-#' @param  FUN_TRANSFO         (optional) [function] model parameters transformation function, if the FUN_MOD used is native in the package FUN_TRANSFO is automatically defined
-#' @param  quiet               (optional) [boolean] boolean indicating if the function is run in quiet mode or not, default=FALSE
-#_FunctionOutputs_________________________________________________________________________________
-#' @return  [list] list containing the function outputs organised as follows:
-#'          \tabular{ll}{
-#'          \emph{$ParamFinalR  }  \tab   [numeric] parameter set obtained at the end of the calibration \cr
-#'          \emph{$CritFinal    }  \tab   [numeric] error criterion obtained at the end of the calibration \cr
-#'          \emph{$Nruns        }  \tab   [numeric] number of model runs done during the calibration \cr
-#'          \emph{$CritName     }  \tab   [character] name of the calibration criterion \cr
-#'          \emph{$CritBestValue}  \tab   [numeric] theoretical best criterion value \cr
-#'          }
-#**************************************************************************************************
-Calibration_optim <- function(InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_TRANSFO=NULL,quiet=FALSE){
-    
-
-    ##_check_class
-    if(inherits(InputsModel,"InputsModel")==FALSE){ stop("InputsModel must be of class 'InputsModel' \n"); return(NULL); }  
-    if(inherits(RunOptions,"RunOptions")==FALSE){ stop("RunOptions must be of class 'RunOptions' \n"); return(NULL); }  
-    if(inherits(InputsCrit,"InputsCrit")==FALSE){ stop("InputsCrit must be of class 'InputsCrit' \n"); return(NULL); }  
-    if(inherits(CalibOptions,"CalibOptions")==FALSE){ stop("CalibOptions must be of class 'CalibOptions' \n"); return(NULL); }  
-    if(inherits(CalibOptions,"optim")==FALSE){ stop("CalibOptions must be of class 'optim' if Calibration_optim is used \n"); return(NULL); }  
-
-
-    ##_check_FUN_TRANSFO
-    if(is.null(FUN_TRANSFO)){
-      if(identical(FUN_MOD,RunModel_GR4H         )){ FUN_TRANSFO <- TransfoParam_GR4H     ; }
-      if(identical(FUN_MOD,RunModel_GR4J         )){ FUN_TRANSFO <- TransfoParam_GR4J     ; }
-      if(identical(FUN_MOD,RunModel_GR5J         )){ FUN_TRANSFO <- TransfoParam_GR5J     ; }
-      if(identical(FUN_MOD,RunModel_GR6J         )){ FUN_TRANSFO <- TransfoParam_GR6J     ; }
-      if(identical(FUN_MOD,RunModel_GR2M         )){ FUN_TRANSFO <- TransfoParam_GR2M     ; }
-      if(identical(FUN_MOD,RunModel_GR1A         )){ FUN_TRANSFO <- TransfoParam_GR1A     ; }
-      if(identical(FUN_MOD,RunModel_CemaNeige    )){ FUN_TRANSFO <- TransfoParam_CemaNeige; }
-      if(identical(FUN_MOD,RunModel_CemaNeigeGR4J) | identical(FUN_MOD,RunModel_CemaNeigeGR5J) | identical(FUN_MOD,RunModel_CemaNeigeGR6J)){
-        if(identical(FUN_MOD,RunModel_CemaNeigeGR4J)){ FUN1 <- TransfoParam_GR4J; FUN2 <- TransfoParam_CemaNeige; }
-        if(identical(FUN_MOD,RunModel_CemaNeigeGR5J)){ FUN1 <- TransfoParam_GR5J; FUN2 <- TransfoParam_CemaNeige; }
-        if(identical(FUN_MOD,RunModel_CemaNeigeGR6J)){ FUN1 <- TransfoParam_GR6J; FUN2 <- TransfoParam_CemaNeige; }
-        FUN_TRANSFO <- function(ParamIn,Direction){
-          Bool <- is.matrix(ParamIn);
-          if(Bool==FALSE){ ParamIn <- rbind(ParamIn); }
-          ParamOut <- NA*ParamIn;
-          NParam   <- ncol(ParamIn);
-          ParamOut[,         1:(NParam-2)] <- FUN1(ParamIn[,         1:(NParam-2)],Direction);
-          ParamOut[,(NParam-1):NParam    ] <- FUN2(ParamIn[,(NParam-1):NParam    ],Direction);
-          if(Bool==FALSE){ ParamOut <- ParamOut[1,]; }
-          return(ParamOut);
-        }
-      }
-      if(is.null(FUN_TRANSFO)){ stop("FUN_TRANSFO was not found (in Calibration function) \n"); return(NULL);  }
-    }
-
-
-    ##_RunModelAndCrit
-    RunModelAndCrit <- function(par,InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_TRANSFO){
-        ParamT <- NA*CalibOptions$FixedParam;
-        ParamT[CalibOptions$OptimParam] <- par;
-        Param <- FUN_TRANSFO(ParamIn=ParamT,Direction="TR");
-        Param[!CalibOptions$OptimParam] <- CalibOptions$FixedParam[!CalibOptions$OptimParam];
-        OutputsModel <- FUN_MOD(InputsModel=InputsModel,RunOptions=RunOptions,Param=Param);
-        OutputsCrit <- FUN_CRIT(InputsCrit=InputsCrit,OutputsModel=OutputsModel);   
-        return(OutputsCrit$CritValue*OutputsCrit$Multiplier);
-    }
-
-
-    ##_temporary_change_of_Outputs_Sim
-    RunOptions$Outputs_Sim <- RunOptions$Outputs_Cal;  ### this reduces the size of the matrix exchange with fortran and therefore speeds the calibration
-    ##_screenPrint
-    if(!quiet){ 
-      cat(paste("\t Calibration in progress (function optim from the stats package) \n",sep=""));
-    }
-    
-
-    ##_lower_and_upper_limit_values (transformed)
-    RangesR <- CalibOptions$SearchRanges;
-    RangesT <- FUN_TRANSFO(RangesR,"RT");
-    lower   <- RangesT[1,CalibOptions$OptimParam];
-    upper   <- RangesT[2,CalibOptions$OptimParam];
-
-    ##_starting_values (transformed)
-    ParamStartT <- FUN_TRANSFO(CalibOptions$StartParam,"RT");
-    par_start   <- ParamStartT[CalibOptions$OptimParam]; 
-
-
-    ##_calibration
-    RESULT <- optim(par=par_start,fn=RunModelAndCrit,gr=NULL,
-                InputsModel,RunOptions,InputsCrit,CalibOptions,FUN_MOD,FUN_CRIT,FUN_TRANSFO,  ## arguments for the RunModelAndCrit function (other than par)
-                method="L-BFGS-B",lower=lower,upper=upper,control=list(),hessian=FALSE)
-    
-
-    ##_outputs_preparation
-    ParamFinalT <- NA*ParamStartT;
-    ParamFinalT[CalibOptions$OptimParam] <- RESULT$par;
-    ParamFinalR <- FUN_TRANSFO(ParamFinalT,"TR");
-    ParamFinalR[!CalibOptions$OptimParam] <- CalibOptions$FixedParam[!CalibOptions$OptimParam];  
-    CritFinal <- RESULT$value;
-
-    ##_storage_of_crit_info
-    OutputsModel  <- FUN_MOD(InputsModel=InputsModel,RunOptions=RunOptions,Param=ParamFinalR);
-    OutputsCrit   <- FUN_CRIT(InputsCrit=InputsCrit,OutputsModel=OutputsModel);   
-    CritName      <- OutputsCrit$CritName;
-    CritBestValue <- OutputsCrit$CritBestValue;
-    Multiplier    <- OutputsCrit$Multiplier;
-
-    ##_screenPrint
-    if(!quiet){ 
-      if(RESULT$convergence==0){ 
-        cat(paste("\t Calibration completed: \n",sep=""));
-        cat(paste("\t     Param = ",paste(formatC(ParamFinalR,format="f",width=8,digits=3),collapse=" , "),"\n",sep=""));
-        cat(paste("\t     Crit ",format(CritName,width=12,justify="left")," = ",formatC(CritFinal*Multiplier,format="f",digits=4),"\n",sep=""));
-      } else {
-        cat(paste("\t Calibration failed: \n",sep=""));
-        cat(paste("\t     ",RESULT$message,sep=""));
-      }
-    }
-    
-    
-    ##_function_output
-    OutputsCalib <- list(as.double(ParamFinalR),CritFinal*Multiplier,as.integer(RESULT$counts[1]),CritName,CritBestValue);
-    names(OutputsCalib) <- c("ParamFinalR","CritFinal","NRuns","CritName","CritBestValue");
-    class(OutputsCalib) <- c("OutputsCalib","optim");
-    return(OutputsCalib);
-
-
-}
-
-
-
-

R/CreateErrorCrit_GAPX.R

+CreateErrorCrit_GAPX <- function(FUN_TRANSFO) {
+
+  FUN_CRIT <- function(InputsCrit, OutputsModel, warnings = TRUE, verbose = TRUE) {
+    ## Arguments check
+    if (!inherits(OutputsModel, "OutputsModel")) {
+      stop("'OutputsModel' must be of class 'OutputsModel'")
+    }
+
+    OutputsModel$RunOptions$ParamT <- FUN_TRANSFO(OutputsModel$RunOptions$Param, "RT")
+
+    EC <- .ErrorCrit(InputsCrit = InputsCrit, Crit = "GAPX", OutputsModel = OutputsModel, warnings = warnings)
+
+    CritValue <- NA
+
+    if (EC$CritCompute) {
+
+      ParamApr <- EC$VarObs[!EC$TS_ignore]
+      ParamOpt <- EC$VarSim[!EC$TS_ignore]
+
+      ## ErrorCrit
+      Crit <- 1 - sum(((ParamApr - ParamOpt) / 20)^2)^0.5
+
+      if (is.numeric(Crit) & is.finite(Crit)) {
+        CritValue <- Crit
+      }
+
+      ## Verbose
+      if (verbose) {
+        message(sprintf("Crit. %s = %.4f", EC$CritName, CritValue))
+      }
+    }
+
+    ## Output
+    OutputsCrit <- list(CritValue       = CritValue,
+                        CritName        = EC$CritName,
+                        CritBestValue   = EC$CritBestValue,
+                        Multiplier      = EC$Multiplier,
+                        Ind_notcomputed = EC$Ind_TS_ignore)
+
+    class(OutputsCrit) <- c("GAPX", "ErrorCrit")
+    return(OutputsCrit)
+  }
+
+  class(FUN_CRIT) <- c("FUN_CRIT", class(FUN_CRIT))
+
+  return(FUN_CRIT)
+}

R/CreateIniStates.R

+CreateIniStates <- function(FUN_MOD, InputsModel, IsHyst = FALSE, IsIntStore = FALSE,
+                            ProdStore = 350, RoutStore = 90, ExpStore = NULL, IntStore = NULL,
+                            UH1 = NULL, UH2 = NULL,
+                            GCemaNeigeLayers = NULL, eTGCemaNeigeLayers = NULL,
+                            GthrCemaNeigeLayers = NULL, GlocmaxCemaNeigeLayers = NULL,
+                            SD = NULL,
+                            verbose = TRUE) {
+
+
+  ObjectClass <- NULL
+
+  UH1n <- 20L
+  UH2n <- UH1n * 2L
+
+  FUN_MOD <- match.fun(FUN_MOD)
+
+  FeatFUN_MOD <- .GetFeatModel(FUN_MOD = FUN_MOD, DatesR = InputsModel$DatesR)
+  ObjectClass <- FeatFUN_MOD$Class
+
+  if (!"CemaNeige" %in% ObjectClass & IsHyst) {
+    stop("'IsHyst' cannot be TRUE if CemaNeige is not used in 'FUN_MOD'")
+  }
+  if (!(identical(FUN_MOD, RunModel_GR5H) | identical(FUN_MOD, RunModel_CemaNeigeGR5H)) & IsIntStore) {
+    stop("'IsIntStore' cannot be TRUE if GR5H is not used in 'FUN_MOD'")
+  }
+
+  ## check InputsModel
+  if (!inherits(InputsModel, "InputsModel")) {
+    stop("'InputsModel' must be of class 'InputsModel'")
+  }
+  if ("GR" %in% ObjectClass & !inherits(InputsModel, "GR")) {
+    stop("'InputsModel' must be of class 'GR'")
+  }
+  if ("CemaNeige" %in% ObjectClass &
+      !inherits(InputsModel, "CemaNeige")) {
+    stop("'InputsModel' must be of class 'CemaNeige'")
+  }
+
+
+  ## check states
+  if (any(eTGCemaNeigeLayers > 0)) {
+    stop("Positive values are not allowed for 'eTGCemaNeigeLayers'")
+  }
+
+  if (identical(FUN_MOD, RunModel_GR6J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J)) {
+    if (is.null(ExpStore)) {
+      stop("'RunModel_*GR6J' need an 'ExpStore' value")
+    }
+  } else if (!is.null(ExpStore)) {
+    if (verbose) {
+      warning(sprintf("'%s' does not require 'ExpStore'. Value set to NA", FeatFUN_MOD$NameFunMod))
+    }
+    ExpStore <- Inf
+  }
+
+  if (identical(FUN_MOD, RunModel_GR2M)) {
+    if (!is.null(UH1)) {
+      if (verbose) {
+        warning(sprintf("'%s' does not require 'UH1'. Values set to NA", FeatFUN_MOD$NameFunMod))
+      }
+      UH1 <- rep(Inf, UH1n)
+    }
+    if (!is.null(UH2)) {
+      if (verbose) {
+        warning(sprintf("'%s' does not require 'UH2'. Values set to NA", FeatFUN_MOD$NameFunMod))
+      }
+      UH2 <- rep(Inf, UH2n)
+    }
+  }
+
+  if ((identical(FUN_MOD, RunModel_GR5J) | identical(FUN_MOD, RunModel_CemaNeigeGR5J)) & !is.null(UH1)) {
+    if (verbose) {
+      warning(sprintf("'%s' does not require 'UH1'. Values set to NA", FeatFUN_MOD$NameFunMod))
+    }
+    UH1 <- rep(Inf, UH1n)
+  }
+  if (!(identical(FUN_MOD, RunModel_GR5H) | identical(FUN_MOD, RunModel_CemaNeigeGR5H)) & !is.null(IntStore)) {
+    if (verbose) {
+      warning(sprintf("'%s' does not require 'IntStore'. Values set to NA", FeatFUN_MOD$NameFunMod))
+    }
+    IntStore <- Inf
+  }
+
+  if ("CemaNeige" %in% ObjectClass & ! "GR" %in% ObjectClass) {
+    if (!is.null(ProdStore)) {
+      if (verbose) {
+        warning(sprintf("'%s' does not require 'ProdStore'. Values set to NA", FeatFUN_MOD$NameFunMod))
+      }
+    }
+    ProdStore <- Inf
+    if (!is.null(RoutStore)) {
+      if (verbose) {
+        warning(sprintf("'%s' does not require 'RoutStore'. Values set to NA", FeatFUN_MOD$NameFunMod))
+      }
+    }
+    RoutStore <- Inf
+    if (!is.null(ExpStore)) {
+      if (verbose) {
+        warning(sprintf("'%s' does not require 'ExpStore'. Values set to NA", FeatFUN_MOD$NameFunMod))
+      }
+    }
+    ExpStore <- Inf
+    if (!is.null(IntStore)) {
+      if (verbose) {
+        warning(sprintf("'%s' does not require 'IntStore'. Values set to NA", FeatFUN_MOD$NameFunMod))
+      }
+    }
+    IntStore <- Inf
+    if (!is.null(UH1)) {
+      if (verbose) {
+        warning(sprintf("'%s' does not require 'UH1'. Values set to NA", FeatFUN_MOD$NameFunMod))
+      }
+    }
+    UH1 <- rep(Inf, UH1n)
+    if (!is.null(UH2)) {
+      if (verbose) {
+        warning(sprintf("'%s' does not require 'UH2'. Values set to NA", FeatFUN_MOD$NameFunMod))
+      }
+    }
+    UH2 <- rep(Inf, UH2n)
+  }
+  if (IsIntStore & is.null(IntStore)) {
+      stop(sprintf("'%s' need values for 'IntStore'", FeatFUN_MOD$NameFunMod))
+  }
+  if ("CemaNeige" %in% ObjectClass & !IsHyst &
+     (is.null(GCemaNeigeLayers) | is.null(eTGCemaNeigeLayers))) {
+      stop(sprintf("'%s' need values for 'GCemaNeigeLayers' and 'GCemaNeigeLayers'", FeatFUN_MOD$NameFunMod))
+  }
+  if ("CemaNeige" %in% ObjectClass & IsHyst &
+     (is.null(GCemaNeigeLayers) | is.null(eTGCemaNeigeLayers) |
+      is.null(GthrCemaNeigeLayers) | is.null(GlocmaxCemaNeigeLayers))) {
+    stop(sprintf("'%s' need values for 'GCemaNeigeLayers', 'GCemaNeigeLayers', 'GthrCemaNeigeLayers' and 'GlocmaxCemaNeigeLayers'", FeatFUN_MOD$NameFunMod))
+  }
+  if ("CemaNeige" %in% ObjectClass & !IsHyst &
+     (!is.null(GthrCemaNeigeLayers) | !is.null(GlocmaxCemaNeigeLayers))) {
+    if (verbose) {
+      warning(sprintf("'%s' does not require 'GthrCemaNeigeLayers' and 'GlocmaxCemaNeigeLayers'. Values set to NA", FeatFUN_MOD$NameFunMod))
+    }
+    GthrCemaNeigeLayers    <- Inf
+    GlocmaxCemaNeigeLayers <- Inf
+  }
+  if (!"CemaNeige" %in% ObjectClass &
+     (!is.null(GCemaNeigeLayers) | !is.null(eTGCemaNeigeLayers) | !is.null(GthrCemaNeigeLayers) | !is.null(GlocmaxCemaNeigeLayers))) {
+    if (verbose) {
+      warning(sprintf("'%s' does not require 'GCemaNeigeLayers' 'GCemaNeigeLayers', 'GthrCemaNeigeLayers' and 'GlocmaxCemaNeigeLayers'. Values set to NA", FeatFUN_MOD$NameFunMod))
+    }
+    GCemaNeigeLayers       <- Inf
+    eTGCemaNeigeLayers     <- Inf
+    GthrCemaNeigeLayers    <- Inf
+    GlocmaxCemaNeigeLayers <- Inf
+  }
+
+
+  ## set states
+  if ("CemaNeige" %in% ObjectClass) {
+    NLayers <- length(InputsModel$LayerPrecip)
+  } else {
+    NLayers <- 1
+  }
+
+
+  ## manage NULL values
+  if (is.null(ExpStore)) {
+    ExpStore <- Inf
+  }
+  if (is.null(IntStore)) {
+    IntStore <- Inf
+  }
+  if (is.null(UH1)) {
+    if ("hourly"  %in% ObjectClass) {
+      k <- 24
+    } else {
+      k <- 1
+    }
+    UH1 <- rep(Inf, UH1n * k)
+  }
+  if (is.null(UH2)) {
+    if ("hourly"  %in% ObjectClass) {
+      k <- 24
+    } else {
+      k <- 1
+    }
+    UH2 <- rep(Inf, UH2n * k)
+  }
+  if (is.null(GCemaNeigeLayers)) {
+    GCemaNeigeLayers <- rep(Inf, NLayers)
+  }
+  if (is.null(eTGCemaNeigeLayers)) {
+    eTGCemaNeigeLayers <- rep(Inf, NLayers)
+  }
+  if (is.null(GthrCemaNeigeLayers)) {
+    GthrCemaNeigeLayers <- rep(Inf, NLayers)
+  }
+  if (any(is.infinite(GthrCemaNeigeLayers))) {
+    GthrCemaNeigeLayers <- rep(Inf, NLayers)
+  }
+  if (is.null(GlocmaxCemaNeigeLayers)) {
+    GlocmaxCemaNeigeLayers <- rep(Inf, NLayers)
+  }
+  if (any(is.infinite(GlocmaxCemaNeigeLayers))) {
+    GlocmaxCemaNeigeLayers <- rep(Inf, NLayers)
+  }
+
+  # check negative values
+  if (any(ProdStore < 0) | any(RoutStore < 0) | any(IntStore < 0) |
+      any(UH1 < 0) | any(UH2 < 0) |
+      any(GCemaNeigeLayers < 0)) {
+    stop("Negative values are not allowed for any of 'ProdStore', 'RoutStore', 'IntStore', 'UH1', 'UH2', 'GCemaNeigeLayers'")
+  }
+
+
+  ## check length
+  if (!is.numeric(ProdStore) || length(ProdStore) != 1L) {
+    stop("'ProdStore' must be numeric of length one")
+  }
+  if (!is.numeric(RoutStore) || length(RoutStore) != 1L) {
+    stop("'RoutStore' must be numeric of length one")
+  }
+  if (!is.numeric(ExpStore) || length(ExpStore) != 1L) {
+    stop("'ExpStore' must be numeric of length one")
+  }
+  if (!is.numeric(IntStore) || length(IntStore) != 1L) {
+    stop("'IntStore' must be numeric of length one")
+  }
+  if ( "hourly" %in% ObjectClass & (!is.numeric(UH1) || length(UH1) != UH1n * 24)) {
+    stop(sprintf("'UH1' must be numeric of length 480 (%i * 24)", UH1n))
+  }
+  if (!"hourly" %in% ObjectClass & (!is.numeric(UH1) || length(UH1) != UH1n)) {
+    stop(sprintf("'UH1' must be numeric of length %i", UH1n))
+  }
+  if ( "hourly" %in% ObjectClass & (!is.numeric(UH2) || length(UH2) != UH2n * 24)) {
+    stop(sprintf("'UH2' must be numeric of length 960 (%i * 24)", UH2n))
+  }
+  if (!"hourly" %in% ObjectClass & (!is.numeric(UH2) || length(UH2) != UH2n)) {
+    stop(sprintf("'UH2' must be numeric of length %i (2 * %i)", UH2n, UH1n))
+  }
+  if (!is.numeric(GCemaNeigeLayers) || length(GCemaNeigeLayers) != NLayers) {
+    stop(sprintf("'GCemaNeigeLayers' must be numeric of length %i", NLayers))
+  }
+  if (!is.numeric(eTGCemaNeigeLayers) || length(eTGCemaNeigeLayers) != NLayers) {
+    stop(sprintf("'eTGCemaNeigeLayers' must be numeric of length %i", NLayers))
+  }
+  if (IsHyst) {
+    if (!is.numeric(GthrCemaNeigeLayers) || length(GthrCemaNeigeLayers) != NLayers) {
+      stop(sprintf("'eTGCemaNeigeLayers' must be numeric of length %i", NLayers))
+    }
+    if (!is.numeric(GlocmaxCemaNeigeLayers) || length(GlocmaxCemaNeigeLayers) != NLayers) {
+      stop(sprintf("'eTGCemaNeigeLayers' must be numeric of length %i", NLayers))
+    }
+  }
+
+  # SD model state handling
+  if (!is.null(SD)) {
+    if (!inherits(InputsModel, "SD")) {
+      stop("'SD' argument provided and 'InputsModel' is not of class 'SD'")
+    }
+    if (!is.list(SD)) {
+      stop("'SD' argument must be a list")
+    }
+    lapply(SD, function(x) {
+      if (!is.numeric(x)) stop("Each item of 'SD' list argument must be numeric")
+    })
+    if (length(SD) != length(InputsModel$LengthHydro)) {
+      stop("Number of items of 'SD' list argument must be the same as the number of upstream connections",
+           sprintf(" (%i required, found %i)", length(InputsModel$LengthHydro), length(SD)))
+    }
+  }
+
+  ## format output
+  IniStates <- list(Store = list(Prod = ProdStore, Rout = RoutStore, Exp = ExpStore, Int = IntStore),
+                    UH = list(UH1 = UH1, UH2 = UH2),
+                    CemaNeigeLayers = list(G = GCemaNeigeLayers, eTG = eTGCemaNeigeLayers,
+                                           Gthr = GthrCemaNeigeLayers, Glocmax = GlocmaxCemaNeigeLayers))
+  IniStatesNA <- unlist(IniStates)
+  IniStatesNA[is.infinite(IniStatesNA)] <- NA
+  IniStatesNA <- relist(IniStatesNA, skeleton = IniStates)
+
+  if (!is.null(SD)) {
+    IniStatesNA$SD <- SD
+  }
+
+  class(IniStatesNA) <- c("IniStates", ObjectClass)
+  if (IsHyst) {
+    class(IniStatesNA) <- c(class(IniStatesNA), "hysteresis")
+  }
+  if (IsIntStore) {
+    class(IniStatesNA) <- c(class(IniStatesNA), "interception")
+  }
+
+  return(IniStatesNA)
+
+
+}

R/CreateInputsCrit.R

-#*************************************************************************************************
-#' Creation of the InputsCrit object required to the ErrorCrit functions.
-#'
-#' Users wanting to use FUN_CRIT functions that are not included in 
-#' the package must create their own InputsCrit object accordingly.
-#*************************************************************************************************
-#' @title  Creation of the InputsCrit object required to the ErrorCrit functions
-#' @author Laurent Coron (June 2014)
-#' @seealso \code{\link{RunModel}}, \code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}}, \code{\link{CreateCalibOptions}}
-#' @example tests/example_ErrorCrit.R
-#' @encoding UTF-8
-#' @export
-#_FunctionInputs__________________________________________________________________________________
-#' @param  FUN_CRIT     [function] error criterion function (e.g. ErrorCrit_RMSE, ErrorCrit_NSE)
-#' @param  InputsModel  [object of class \emph{InputsModel}] see \code{\link{CreateInputsModel}} for details
-#' @param  RunOptions   [object of class \emph{RunOptions}] see \code{\link{CreateRunOptions}} for details
-#' @param  Qobs         [numeric] series of observed discharges [mm]
-#' @param  BoolCrit     (optional) [boolean] boolean giving the time steps to consider in the computation (all time steps are consider by default)
-#' @param  transfo      (optional) [character] name of the transformation (e.g. "", "sqrt", "log", "inv", "sort")
-#' @param  Ind_zeroes   (optional) [numeric] indices of the time-steps where zeroes are observed
-#' @param  epsilon      (optional) [numeric] epsilon to add to all Qobs and Qsim if \emph{$Ind_zeroes} is not empty
-#_FunctionOutputs_________________________________________________________________________________
-#' @return  [list] object of class \emph{InputsCrit} containing the data required to evaluate the model outputs; it can include the following:
-#'          \tabular{ll}{
-#'          \emph{$BoolCrit  }  \tab   [boolean] boolean giving the time steps to consider in the computation \cr
-#'          \emph{$Qobs      }  \tab   [numeric] series of observed discharges [mm] \cr
-#'          \emph{$transfo   }  \tab   [character] name of the transformation (e.g. "", "sqrt", "log", "inv", "sort") \cr
-#'          \emph{$Ind_zeroes}  \tab   [numeric] indices of the time-steps where zeroes are observed \cr
-#'          \emph{$epsilon   }  \tab   [numeric] epsilon to add to all Qobs and Qsim if \emph{$Ind_zeroes} is not empty \cr
-#'          }
-#**************************************************************************************************
-CreateInputsCrit <- function(FUN_CRIT,InputsModel,RunOptions,Qobs,BoolCrit=NULL,transfo="",Ind_zeroes=NULL,epsilon=NULL){
-
-  ObjectClass <- NULL;
-
-  ##check_FUN_CRIT
-    BOOL <- FALSE;
-    if(identical(FUN_CRIT,ErrorCrit_NSE) | identical(FUN_CRIT,ErrorCrit_KGE) | identical(FUN_CRIT,ErrorCrit_KGE2) | 
-       identical(FUN_CRIT,ErrorCrit_RMSE)){
-      BOOL <- TRUE; }
-    if(!BOOL){ stop("incorrect FUN_CRIT for use in CreateInputsCrit \n"); return(NULL); } 
-
-  ##check_arguments
-    if(inherits(InputsModel,"InputsModel")==FALSE){ stop("InputsModel must be of class 'InputsModel' \n" ); return(NULL); } 
-    if(inherits(RunOptions ,"RunOptions" )==FALSE){ stop("RunOptions must be of class 'RunOptions' \n" ); return(NULL); } 
-    LLL <- length(InputsModel$DatesR[RunOptions$IndPeriod_Run])
-
-    if(is.null(Qobs)    ){ stop("Qobs is missing \n"); return(NULL); } 
-    if(!is.vector( Qobs)){ stop(paste("Qobs must be a vector of numeric values \n",sep="")); return(NULL); }
-    if(!is.numeric(Qobs)){ stop(paste("Qobs must be a vector of numeric values \n",sep="")); return(NULL); }
-    if(length(Qobs)!=LLL){ stop("Qobs and InputsModel series must have the same length \n"); return(NULL); } 
-
-    if(is.null(BoolCrit)){ BoolCrit <- rep(TRUE,length(Qobs)); }
-    if(!is.logical(BoolCrit)){ stop("BoolCrit must be a vector of boolean \n" ); return(NULL); } 
-    if(length(BoolCrit)!=LLL){ stop("BoolCrit and InputsModel series must have the same length \n"); return(NULL); } 
-
-    if(is.null(transfo)      ){ stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' \n"); return(NULL); } 
-    if(!is.vector(transfo   )){ stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' \n"); return(NULL); } 
-    if(length(transfo)!=1    ){ stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' \n"); return(NULL); } 
-    if(!is.character(transfo)){ stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' \n"); return(NULL); } 
-    if(transfo %in% c("","sqrt","log","inv") == FALSE){
-                                stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' \n"); return(NULL); } 
-
-    if(!is.null(Ind_zeroes)){
-      if(!is.vector( Ind_zeroes)){ stop("Ind_zeroes must be a vector of integers \n" ); return(NULL); } 
-      if(!is.integer(Ind_zeroes)){ stop("Ind_zeroes must be a vector of integers \n" ); return(NULL); } 
-    }
-    if(!is.null(epsilon)){
-      if(!is.vector( epsilon) | length(epsilon)!=1 | !is.numeric(epsilon)){ 
-        stop("epsilon must be single numeric value \n" ); return(NULL); }
-      epsilon=as.double(epsilon);
-    }
-
-  ##Create_InputsCrit
-    InputsCrit <- list(BoolCrit=BoolCrit,Qobs=Qobs,transfo=transfo,Ind_zeroes=Ind_zeroes,epsilon=epsilon);
-    class(InputsCrit) <- c("InputsCrit",ObjectClass);
-    return(InputsCrit);
+CreateInputsCrit <- function(FUN_CRIT,
+                             InputsModel,
+                             RunOptions,
+                             Obs,
+                             VarObs = "Q",
+                             BoolCrit = NULL,
+                             transfo = "",
+                             Weights = NULL,
+                             epsilon = NULL,
+                             warnings = TRUE) {
 
 
-}
+  ObjectClass <- NULL
+
+
+  ## ---------- check arguments
+
+  ## check 'InputsModel'
+  if (!inherits(InputsModel, "InputsModel")) {
+    stop("'InputsModel' must be of class 'InputsModel'")
+  }
+
+
+  ## length of index of period to be used for the model run
+  LLL <- length(InputsModel$DatesR[RunOptions$IndPeriod_Run])
+
+
+  ## check 'Obs' and definition of idLayer
+  if (!is.numeric(unlist(Obs))) {
+    stop("'Obs' must be a (list of) vector(s) of numeric values")
+  }
+  Obs2 <- Obs
+  if ("ParamT" %in% VarObs) {
+    if (is.list(Obs2)) {
+      Obs2[[which(VarObs == "ParamT")]] <- NULL
+    } else {
+      Obs2 <- NULL
+    }
+  }
+  if (!is.null(Obs2)) {
+    vecObs <- unlist(Obs2)
+    if (length(vecObs) %% LLL != 0) {
+      stop(sprintf("'Obs' must be a (list of) vector(s) of numeric values of length %i", LLL), call. = FALSE)
+    }
+  }
+  if (!is.list(Obs)) {
+    idLayer <- list(1L)
+    Obs <- list(Obs)
+  } else {
+    idLayer <- lapply(Obs, function(i) {
+      if (is.list(i)) {
+        length(i)
+      } else {
+        1L
+      }
+    })
+    Obs <- lapply(Obs, function(x) rowMeans(as.data.frame(x)))
+  }
+
+
+  ## create list of arguments
+  listArgs <- list(FUN_CRIT   = FUN_CRIT,
+                   Obs        = Obs,
+                   VarObs     = VarObs,
+                   BoolCrit   = BoolCrit,
+                   idLayer    = idLayer,
+                   transfo    = as.character(transfo),
+                   Weights    = Weights,
+                   epsilon    = epsilon)
+
+
+  ## check lists lengths
+  for (iArgs in names(listArgs)) {
+    if (iArgs %in% c("Weights", "BoolCrit", "epsilon")) {
+      if (any(is.null(listArgs[[iArgs]]))) {
+        listArgs[[iArgs]] <- lapply(seq_along(listArgs$FUN_CRIT), function(x) NULL)
+      }
+    }
+    if (iArgs %in% c("FUN_CRIT", "VarObs", "transfo", "Weights") & length(listArgs[[iArgs]]) > 1L) {
+      listArgs[[iArgs]] <- as.list(listArgs[[iArgs]])
+    }
+    if (!is.list(listArgs[[iArgs]])) {
+      listArgs[[iArgs]] <- list(listArgs[[iArgs]])
+    }
+  }
+
+  ## check 'FUN_CRIT'
+  listArgs$FUN_CRIT <- lapply(listArgs$FUN_CRIT, FUN = match.fun)
+
 
+  ## check 'VarObs'
+  if (missing(VarObs)) {
+    listArgs$VarObs <- as.list(rep("Q", times = length(listArgs$Obs)))
+    # if (warnings) {
+    #   warning("'VarObs' automatically set to \"Q\"")
+    # }
+  }
+
+
+  ## check 'VarObs' + 'RunOptions'
+  if ("Q" %in% VarObs & !inherits(RunOptions, "GR")) {
+    stop("'VarObs' cannot contain Q if a GR rainfall-runoff model is not used")
+  }
+  if (any(c("SCA", "SWE") %in% VarObs) & !inherits(RunOptions, "CemaNeige")) {
+    stop("'VarObs' cannot contain SCA or SWE if CemaNeige is not used")
+  }
+  if ("SCA" %in% VarObs & inherits(RunOptions, "CemaNeige") & !"Gratio"   %in% RunOptions$Outputs_Sim) {
+    stop("'Gratio' is missing in 'Outputs_Sim' of 'RunOptions', which is necessary to output SCA with CemaNeige")
+  }
+  if ("SWE" %in% VarObs & inherits(RunOptions, "CemaNeige") & !"SnowPack" %in% RunOptions$Outputs_Sim) {
+    stop("'SnowPack' is missing in 'Outputs_Sim' of 'RunOptions', which is necessary to output SWE with CemaNeige")
+  }
+
+
+  ## check 'transfo'
+  if (missing(transfo)) {
+    listArgs$transfo <- as.list(rep("", times = length(listArgs$Obs)))
+    # if (warnings) {
+    #   warning("'transfo' automatically set to \"\"")
+    # }
+  }
+
+  ## check length of each args
+  if (length(unique(sapply(listArgs, FUN = length))) != 1) {
+    stopListArgs <- paste(sapply(names(listArgs), shQuote), collapse = ", ")
+    stop(sprintf("arguments %s must have the same length", stopListArgs))
+  }
+
+
+  ## check 'RunOptions'
+  if (!inherits(RunOptions , "RunOptions")) {
+    stop("'RunOptions' must be of class 'RunOptions'")
+  }
+
+
+  ## check 'Weights'
+  if (length(listArgs$Weights) > 1 & sum(unlist(listArgs$Weights)) == 0 & !any(sapply(listArgs$Weights, is.null))) {
+    stop("sum of 'Weights' cannot be equal to zero")
+  }
+
+
+  ## ---------- reformat
+
+  ## reformat list of arguments
+  listArgs2 <- lapply(seq_along(listArgs$FUN_CRIT), function(i) lapply(listArgs, "[[", i))
+
+  ## preparation of warning messages
+  inVarObs  <- c("Q", "SCA", "SWE", "ParamT")
+  msgVarObs <- "'VarObs' must be a (list of) character vector(s) and one of %s"
+  msgVarObs <- sprintf(msgVarObs, paste(sapply(inVarObs, shQuote), collapse = ", "))
+  inTransfo  <- c("", "sqrt", "log", "inv", "sort", "boxcox") # pow is not checked by inTransfo, but appears in the warning message and checkef after (see ## check 'transfo')
+  msgTransfo <- "'transfo' must be a (list of) character vector(s) and one of %s, or numeric value for power transformation"
+  msgTransfo <- sprintf(msgTransfo, paste(sapply(inTransfo, shQuote), collapse = ", "))
+
+
+  ## ---------- loop on the list of inputs
+
+  InputsCrit <- lapply(listArgs2, function(iListArgs2) {
+
+    ## define FUN_CRIT as a character string
+    iListArgs2$FUN_CRIT <- match.fun(iListArgs2$FUN_CRIT)
+
+    ## check 'FUN_CRIT'
+    if (!all(class(iListArgs2$FUN_CRIT) == c("FUN_CRIT", "function"))) {
+      stop("incorrect 'FUN_CRIT' for use in 'CreateInputsCrit'", call. = FALSE)
+    }
+    if (identical(iListArgs2$FUN_CRIT, ErrorCrit_RMSE) & length(listArgs$Weights) > 1 & all(!is.null(unlist(listArgs$Weights)))) {
+      stop("calculating a composite criterion with the RMSE is not allowed since RMSE is not a dimensionless metric", call. = FALSE)
+    }
+
+    ## check 'Obs'
+    if (iListArgs2$VarObs == "ParamT") {
+      # Parameter for regularisation
+      L2 <- RunOptions$FeatFUN_MOD$NbParam
+    } else {
+      # Observation time series
+      L2 <- LLL
+    }
+    if (!is.vector(iListArgs2$Obs) | length(iListArgs2$Obs) != L2 | !is.numeric(iListArgs2$Obs)) {
+      stop(sprintf("'Obs' must be a (list of) vector(s) of numeric values of length %i", L2), call. = FALSE)
+    }
+
+    ## check 'BoolCrit'
+    if (is.null(iListArgs2$BoolCrit)) {
+      iListArgs2$BoolCrit <- rep(TRUE, length(iListArgs2$Obs))
+    }
+    if (!is.logical(iListArgs2$BoolCrit)) {
+      stop("'BoolCrit' must be a (list of) vector(s) of boolean", call. = FALSE)
+    }
+    if (length(iListArgs2$BoolCrit) != L2) {
+      stop("'BoolCrit' and the period defined in 'RunOptions' must have the same length", call. = FALSE)
+    }
+
+    ## check 'VarObs'
+    if (!is.vector(iListArgs2$VarObs) | length(iListArgs2$VarObs) != 1 | !is.character(iListArgs2$VarObs) | !all(iListArgs2$VarObs %in% inVarObs)) {
+      stop(msgVarObs, call. = FALSE)
+    }
+
+    ## check 'VarObs' + 'Obs'
+    if (any(iListArgs2$VarObs %in% "SCA")) {
+      idSCA <- which(iListArgs2$VarObs == "SCA")
+      if (length(idSCA) == 1L) {
+        vecSCA <- iListArgs2$Obs
+      } else {
+        vecSCA <- unlist(iListArgs2$Obs[idSCA])
+      }
+      if (min(vecSCA, na.rm = TRUE) < 0 | max(vecSCA, na.rm = TRUE) > 1) {
+        stop("'Obs' outside [0,1] for \"SCA\"", call. = FALSE)
+      }
+    }
+    inPosVarObs <- c("Q", "SWE")
+    if (any(iListArgs2$VarObs %in% inPosVarObs)) {
+      idQSS <- which(iListArgs2$VarObs %in% inPosVarObs)
+      if (length(idQSS) == 1L) {
+        vecQSS <- iListArgs2$Obs
+      } else {
+        vecQSS <- unlist(iListArgs2$Obs[idQSS])
+      }
+      if (all(is.na(vecQSS))) {
+        stop("'Obs' contains only missing values", call. = FALSE)
+      }
+      if (min(vecQSS, na.rm = TRUE) < 0) {
+        stop(sprintf("'Obs' outside [0,Inf[ for \"%s\"", iListArgs2$VarObs), call. = FALSE)
+      }
+    }
+
+
+    ## check 'transfo'
+    if (is.null(iListArgs2$transfo) | !is.vector(iListArgs2$transfo) | length(iListArgs2$transfo) != 1 | !is.character(iListArgs2$transfo)) {
+      stop(msgTransfo, call. = FALSE)
+    }
+    isNotInTransfo <- !(iListArgs2$transfo %in% inTransfo)
+    if (any(isNotInTransfo)) {
+      powTransfo <- iListArgs2$transfo[isNotInTransfo]
+      powTransfo <- gsub("\\^|[[:alpha:]]", "", powTransfo)
+      numExpTransfo <- suppressWarnings(as.numeric(powTransfo))
+      if (any(is.na(numExpTransfo))) {
+        stop(msgTransfo, call. = FALSE)
+      }
+      iListArgs2$transfo <- paste0("^", iListArgs2$transfo)
+    }
+
+    ## check 'Weights'
+    if (!is.null(iListArgs2$Weights)) {
+      if (!is.vector(iListArgs2$Weights) | length(iListArgs2$Weights) != 1 | !is.numeric(iListArgs2$Weights) | any(iListArgs2$Weights < 0)) {
+        stop("'Weights' must be a single (list of) positive or equal to zero value(s)", call. = FALSE)
+      }
+    }
+
+    ## check 'epsilon'
+    if (!is.null(iListArgs2$epsilon)) {
+      if (!is.vector(iListArgs2$epsilon) | length(iListArgs2$epsilon) != 1 | !is.numeric(iListArgs2$epsilon) | any(iListArgs2$epsilon <= 0)) {
+        stop("'epsilon' must be a single (list of) positive value(s)", call. = FALSE)
+      }
+    } else if (iListArgs2$transfo %in% c("log", "inv") & any(iListArgs2$Obs %in% 0) & warnings) {
+      warning("zeroes detected in Obs: the corresponding time-steps will be excluded by the 'ErrorCrit*' functions as the epsilon argument was set to NULL", call. = FALSE)
+    }
+
+    ## check 'transfo' + 'FUN_CRIT'
+    if (iListArgs2$transfo == "log" & warnings) {
+      warn_log_kge <- "we do not advise using the %s with a log transformation on Obs (see the details section in the 'CreateInputsCrit' help)"
+      if (identical(iListArgs2$FUN_CRIT, ErrorCrit_KGE)) {
+        warning(sprintf(warn_log_kge, "KGE"), call. = FALSE)
+      }
+      if (identical(iListArgs2$FUN_CRIT, ErrorCrit_KGE2)) {
+        warning(sprintf(warn_log_kge, "KGE'"), call. = FALSE)
+      }
+    }
+
+
+    ## Create InputsCrit
+    iInputsCrit <- list(FUN_CRIT   = iListArgs2$FUN_CRIT,
+                        Obs        = iListArgs2$Obs,
+                        VarObs     = iListArgs2$VarObs,
+                        BoolCrit   = iListArgs2$BoolCrit,
+                        idLayer    = iListArgs2$idLayer,
+                        transfo    = iListArgs2$transfo,
+                        epsilon    = iListArgs2$epsilon,
+                        Weights    = iListArgs2$Weights)
+    class(iInputsCrit) <- c("Single", "InputsCrit", ObjectClass)
+    return(iInputsCrit)
+
+  })
+  names(InputsCrit) <- paste0("IC", seq_along(InputsCrit))
+
+  listVarObs <- sapply(InputsCrit, FUN = "[[", "VarObs")
+  inCnVarObs <- c("SCA", "SWE")
+  if (!"ZLayers" %in% names(InputsModel)) {
+    if (any(listVarObs %in% inCnVarObs)) {
+      stop(sprintf("'VarObs' can not be equal to %i if CemaNeige is not used",
+                   paste(sapply(inCnVarObs, shQuote), collapse = " or ")))
+    }
+  } else {
+    listGroupLayer0 <- sapply(InputsCrit, FUN = "[[", "idLayer")
+    listGroupLayer <- rep(listVarObs, times = listGroupLayer0)
+    tabGroupLayer  <- as.data.frame(table(listGroupLayer))
+    colnames(tabGroupLayer) <- c("VarObs", "freq")
+    nLayers <- length(InputsModel$ZLayers)
+    for (iInCnVarObs in inCnVarObs) {
+      if (any(listVarObs %in% iInCnVarObs)) {
+        if (tabGroupLayer[tabGroupLayer$VarObs %in% iInCnVarObs, "freq"] != nLayers) {
+          stop(sprintf("'Obs' must contain %i vector(s) about %s", nLayers, iInCnVarObs))
+        }
+      }
+    }
+  }
+
+  ## define idLayer as an index of the layer to use
+  for (iInCnVarObs in unique(listVarObs)) {
+    if (!iInCnVarObs %in% inCnVarObs) {
+      for (i in which(listVarObs == iInCnVarObs)) {
+        InputsCrit[[i]]$idLayer <- NA
+      }
+    } else {
+      aa <- listGroupLayer0[listVarObs == iInCnVarObs]
+      aa <- unname(aa)
+      bb <- cumsum(c(0, aa[-length(aa)]))
+      cc <- lapply(seq_along(aa), function(x) seq_len(aa[x]) + bb[x])
+      k <- 1
+      for (i in which(listVarObs == iInCnVarObs)) {
+        InputsCrit[[i]]$idLayer <- cc[[k]]
+        k <- k + 1
+      }
+    }
+  }
+
+
+  ## if only one criterion --> not a list of InputsCrit but directly an InputsCrit
+  if (length(InputsCrit) < 2) {
+    InputsCrit <- InputsCrit[[1L]]
+    InputsCrit["Weights"] <- list(Weights = NULL)
+  } else {
+    if (any(sapply(listArgs$Weights, is.null))) {
+      for (iListArgs in InputsCrit) {
+        iListArgs$Weights <- NULL
+      }
+      class(InputsCrit) <- c("Multi", "InputsCrit", ObjectClass)
+    } else {
+      class(InputsCrit) <- c("Compo", "InputsCrit", ObjectClass)
+    }
+    combInputsCrit <- combn(x = length(InputsCrit), m = 2)
+    apply(combInputsCrit, MARGIN = 2, function(i) {
+      equalInputsCrit <- identical(InputsCrit[[i[1]]], InputsCrit[[i[2]]])
+      if (equalInputsCrit) {
+        warning(sprintf("elements %i and %i of the criteria list are identical. This might not be necessary", i[1], i[2]), call. = FALSE)
+      }
+    })
+  }
+
+  return(InputsCrit)
+
+}

R/CreateInputsCrit_Lavenne.R

+CreateInputsCrit_Lavenne <- function(FUN_CRIT = ErrorCrit_KGE,
+                                      InputsModel,
+                                      RunOptions,
+                                      Obs,
+                                      VarObs = "Q",
+                                      AprParamR,
+                                      AprCrit = 1,
+                                      k = 0.15,
+                                      BoolCrit = NULL,
+                                      transfo = "sqrt",
+                                      epsilon = NULL) {
+
+  # Check parameters
+  if (!is.numeric(AprCrit) || length(AprCrit) != 1 || AprCrit > 1) {
+    stop("'AprCrit' must be a numeric of length 1 with a maximum value of 1")
+  }
+  if (!is.numeric(k) || length(k) != 1 || k < 0 || k > 1) {
+    stop("'k' must be a numeric of length 1 with a value between 0 and 1")
+  }
+  if (!is.null(BoolCrit) && !is.logical(BoolCrit)) {
+    stop("'BoolCrit must be logical")
+  }
+  if (!is.character(transfo)) {
+    stop("'transfo' must be character")
+  }
+  if (!is.null(epsilon) && !is.numeric(epsilon)) {
+    stop("'epsilon' must be numeric")
+  }
+  if (!is.numeric(AprParamR) || length(AprParamR) != RunOptions$FeatFUN_MOD$NbParam) {
+    stop("'AprParamR' must be a numeric vector of length ",
+         RunOptions$FeatFUN_MOD$NbParam)
+  }
+
+
+  FUN_TRANSFO <- .FunTransfo(RunOptions$FeatFUN_MOD)
+
+  AprParamT <- FUN_TRANSFO(AprParamR, "RT")
+
+  ErrorCrit_GAPX <- CreateErrorCrit_GAPX(FUN_TRANSFO)
+
+
+
+  CreateInputsCrit(FUN_CRIT = list(FUN_CRIT, ErrorCrit_GAPX),
+                   InputsModel = InputsModel,
+                   RunOptions = RunOptions,
+                   Obs = list(Obs, AprParamT),
+                   VarObs = c("Q", "ParamT"),
+                   Weights = c(1 - k, k * max(0, AprCrit)),
+                   BoolCrit = list(BoolCrit, NULL),
+                   transfo = list(transfo, ""),
+                   epsilon = list(epsilon, NULL))
+}