.Rbuildignore

@@ -2,3 +2,14 @@
 ^\.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
-packrat/lib*/
+
+# 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: 1.0.15.3
-Date: 2018-10-15
+Version: 1.7.6.9000
+Date: 2023-10-25
 Authors@R: c(
   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("Olivier", "Delaigue", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7668-8468"), email = "airGR@irstea.fr"),
-  person("Guillaume", "Thirel", role = c("aut"), comment = c(ORCID = "0000-0002-1444-1830")),
   person("Claude", "Michel", role = c("aut", "ths")),
   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", vignette = "'Parameter estimation' vignettes")),
+  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("Audrey", "Valéry", role = c("ctb"))
   )
-Depends: R (>= 3.0.1)
-Suggests: knitr, rmarkdown, coda, DEoptim, dplyr, FME, ggmcmc, hydroPSO, Rmalschains
-Description: Hydrological modelling tools developed at Irstea-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
+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: https://webgr.irstea.fr/en/airGR/
+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

@@ -8,7 +8,13 @@ useDynLib(airGR, .registration = TRUE)
 #####################################
 ##            S3 methods           ##
 #####################################
-S3method("plot", "OutputsModel")
+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)
 
 
 
@@ -18,8 +24,10 @@ S3method("plot", "OutputsModel")
 export(Calibration)
 export(Calibration_Michel)
 export(CreateCalibOptions)
+export(CreateErrorCrit_GAPX)
 export(CreateIniStates)
 export(CreateInputsCrit)
+export(CreateInputsCrit_Lavenne)
 export(CreateInputsModel)
 export(CreateRunOptions)
 export(DataAltiExtrapolation_Valery)
@@ -28,30 +36,38 @@ 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(plot_OutputsModel)
-
+export(TransfoParam_Lag)
+#export(.ErrorCrit)
+#export(.FeatModels)
 
 
 #####################################

NEWS.md

+## Release History of the airGR Package
+
+
+
+### 1.7.6 Release Notes (2023-10-25)
+
+#### Bug fixes
+
+- `CreateCalibOptions()` now uses parameter screening for `RunModel_Lag()` which are now expressed in the transformed space instead of the parameter space. ([#156](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/156))
+- `RunModel_CemaNeige*()` now takes into account the case when `dG = 0`. ([#178](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/178))
+
+
+#### Minor user-visible changes
+
+- `Calibration_Michel()` now runs faster as the `ProposeCandidatesGrid()` was improved to create the propose candidates grid. ([#157](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/157)) 
+- `TransfoParamGR5J()` now returns the correct  error message when the number of parameters is incorrect. ([#168](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/168)) 
+
+
+#### CRAN-compatibility updates
+
+- `frun_*` Fortran subroutine does not use anymore the 'DLLEXPORT' command. ([#180](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/180))
+- The 'Rmalschains' package is back on CRAN and it is again suggested (cf. the 'param_optim' vignette). ([#175](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/175))
+- The 'hydroPSO' package is no longer suggested (but the code linked to its use and is always present in the 'param_optim' vignette). ([#182](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/182))
+
+____________________________________________________________________________________
+
+
+### 1.7.4 Release Notes (2023-04-11)
+
+#### CRAN-compatibility updates
+
+- The 'Rmalschains' package is no longer suggested (but the code linked to its use and is always present in the 'param_optim' vignette). ([#172](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/172))
+- `.ErrorCrit()` and `.FeatModels` function are no more exported. ([#173](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/173))
+
+____________________________________________________________________________________
+
+
+### 1.7.0 Release Notes (2022-02-21)
+
+#### New features
+
+- Semi-distributed modelling mode can now use the regularisation calibration proposed by [Lavenne et al. (2019)](https://doi.org/10.1029/2018WR024266). Added the `CreateInputsCrit_Lavenne()` to define a composite criterion based on the formula. Added the `CreateErrorCrit_GAPX()` function to compute an error criterion based on the GAPX formula. ([#111](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/111))
+- `OutputsModel`, returned by the `RunModel_*GR*()` function, gains a `RunOptions` element which is a list and contains 2 sub-elements: `WarmUpQsim` (vector series of simulated discharge on the warm-up period) and `Param` (vector of the model parameter values). ([#123](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/123))
+- `plot.OutputsModel()` gains a `AxisTS` argument in order to manage x-axis representing calendar dates and times. It avoids to display ugly x-axis. ([#122](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/122))
+
+
+#### Deprecated and defunct
+
+- The deprecated `LatRad` argument has been removed from the `PEdaily_Oudin()` function. ([#81](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/81))
+- The deprecated `Qobs` argument has been removed from the `CreateInputsCrit()` function. ([#81](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/81))
+- The deprecated `Ind_zeroes` argument has been removed from the `CreateInputsCrit()` function. ([#81](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/81))
+- The deprecated `verbose` argument has been removed from the `CreateInputsCrit()` function. ([#81](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/81))
+- The deprecated `FUN_CRIT` argument has been removed from the `ErrorCrit()` function. ([#81](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/81))
+
+
+#### Bug fixes
+
+- `SeriesAggreg()` now correctly reorders regime time series when the monthly regime is computed from a time series that does not start in January. It also keeps original `data.frame` column names. ([#133](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/133))
+- `DataAltiExtrapolation_Valery()` now correctly extract HypsoData values for each elevation layers. The selected indices were wrong (one less than expected) ([#144](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/144))
+- `CreateIniStates()` does not return anymore an error message when `IntStore` is set and `RunModel_GR5H` is used. ([#144](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/145))
+
+
+#### Major user-visible changes
+
+- `RunModel_Lag()` now handles warm-up period simulation (set in `CreateRunOptions()`). ([#132](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/132))
+
+
+#### Minor user-visible changes
+
+- `PE_Oudin()` can use inconsistent time series. It allows to mixing time series from different stations. ([#134](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/134))
+- Added the use of `.GetFeatModel()` in `CreateCalibOptions()` and `CreateIniStates()` functions in order to simplified their codes. ([#111](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/111))
+- Added the `.FunTransfo` in order to manage the parameter transformations and to simplified the code of the `CreateCalibOptions()` function ([#111](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/111))
+- Added the `.ArgumentsCheckGR()` function in order to check the arguments of the` RunModel_*()` functions and simplified their codes. ([#129](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/129))
+- Added the `.GetOutputsModelGR()` function in order to manage the outputs of the` RunModel_*()` functions and simplified their codes. ([#129](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/129))
+- The code of the `plot.OutputsModel()` function has been slightly simplified. ([#122](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/122), [#147](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/147))
+
+
+#### Version control and issue tracking
+
+- Added tests to check that the parameter sets returned by calibration algorithm do not change for any of the models. ([#120](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/120))
+- Added tests to detect Decreased performance of calibration execution time. ([#136](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/136))
+- Fixed the reverse package dependencies checked by the CI pipelines. ([#146](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/146))
+
+____________________________________________________________________________________
+
+
+### 1.6.12 Release Notes (2021-04-27)
+
+#### New features
+
+- `CreateInputsModel()` gains a `QupstrUnit` argument in order to manage the unit of the flow in the `Qupstream` argument in case of the use of a semi-distributed version of a hydrological model. ([#110](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/110))
+- `RunModel_Lag()` gains a `QcontribDown` argument containing the time series of the runoff contribution of the downstream sub-basin in case of the use of a semi-distributed version of a hydrological model. ([#109](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/109))
+
+
+#### Bug fixes
+
+- Fixed bug in `RunModel`. The `RunModel_Lag()` can now be passed to the `FUN_MOD` argument. ([#108](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/108))
+- Fixed bug in `RunModel_Lag()`. The function no longer returns two values for a single time step run. ([#102](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/102))
+- Fixed bug in `RunModel_Lag()`. The `StateEnd` value is now correct when there are more than a single upstream basin. ([#103](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/103))
+- Fixed bug in `RunModel_Lag()`. The `StateEnd` value is now correct when the upstream flow unit is mm/time step. ([#104](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/104))
+- Fixed bug in `RunModel_CemaNeigeGR5H()`. The solid precipitation are now taken into account in the GR5H model. ([#105](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/105))
+- Fixed bug in `RunModel_CemaNeige()` and `CreateInputsModel()`. `RunModel_CemaNeige()` now runs at the hourly time step. ([#106](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/106))
+- Fixed the 'param_optim' vignette. The starting points used for the multi-start approach are now in the transformed space.([#101](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/101))
+
+
+#### Major user-visible changes
+
+- `LengthHydro` must now be set in kilometers (not anymore in meters) in the `CreateInputsModel()` function. ([#112](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/112))
+- `TransfoParam_GR5H()` now use the same transformation as `TransfoParam_GR4H()` for the X1 parameter. The previous transformation set by Ficchì seems unnecessary as it provokes irrealistically high X1 values. ([#50](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/50))
+
+
+#### Minor user-visible changes
+
+- The `RunModel*()` functions now run faster. The computation times are significantly shorter for long times series with many time steps (e.g. hourly times series), due to a better management of the missing values in and out the Fortran codes. Only simulation computation times have been improved (it is largely invisible to the user for calibration computation times). ([#113](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/113))
+- The external calibration algorithms used in 'param_optim' and 'param_mcmc' vignettes now run faster. The `RunModel_*()` functions used during the parameter estimation process now run faster because the outputs contain only the simulated flows (see the `Outputs_Sim` argument in the `CreateRunOptions()` help page).
+- Added `.FeatModels()` and `.GetFeatModel()` functions in order to repectively store and get model features (e.g. name, number of parameters, time unit). Therefore the codes of the `CreateInputsModel()` and the `CreateRunOptions()` functions have been simplified. ([#106](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/106))
+
+
+#### Version control and issue tracking
+
+- The CI pipelines now fail when the checks return a warning message (and not just an error message). ([#86](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/86))
+- The reverse dependencies packages (e.g. the 'airGRteaching' or the 'airGRdatassim') are now checked by the CI pipelines. ([#86](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/86))
+
+____________________________________________________________________________________
+
+
+### 1.6.10.4 Release Notes (2021-01-29)
+
+#### New features
+
+- Added a section 'param_optim' vignette to explain how to manage with multiobjective optimization using the 'caRamel' package. ([#61](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/61))
+
+
+#### Major user-visible changes
+
+- `Imax()` now returns an error message when `IndPeriod_Run` doesn't select 24 hours by day, instead of `numeric(0)`. ([#92](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/92))
+
+
+#### Minor user-visible changes
+
+- Fixed warning returned by GCC Fortran when compiling `frun_GR5H.f90`. ([#93](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/93))
+
+
+#### CRAN-compatibility updates
+
+- Coerce `character` dates into `POSIXlt` in `RunModel_GR1A()` example and in `SeriesAggreg()` tests in order to avoid bad subsetting on time series due to mixing UTC and local time (error returned on macOS flavors). ([#94](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/94))
+
+____________________________________________________________________________________
+
+
+### 1.6.9.27 Release Notes (2021-01-18)
+
+#### New features
+
+- Added `SeriesAggreg` S3 method with functions for `InputsModel`, `OutputsModel`, `list`, `data.frame` class objects. This new version of the `SeriesAggreg()` function also allows to compute regimes. ([#25](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/25))
+- Added `.GetAggregConvertFun()` private function in order to choose automatically the `ConvertFun` to apply on each element of objects used in `SeriesAggreg.InputsModel()` and `SeriesAggreg.OutputsModel()`.
+- Added `.AggregConvertFunTable` data.frame that allows the user to see what names of list items or data.frame column names are guessed and eventually customise this correspondence table.
+- `PE_Oudin()` now presents a `RunFortran` argument to run the code in Fortran or in R. The Fortran mode is the fastest. ([#62](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/62))
+- Added `RunModel_Lag()` which allows to perform a single run for the Lag model over the test period in order to run semi-distributed GR models. ([#34](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/34))
+- Added the 'sd_model' vignette to explain how to manage the use of semi-distributed GR models. ([#34](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/34))
+- Added `[` S3 method for `InputsModel` class object in order to extract subsets of it. ([#67](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/67))
+
+
+#### Deprecated and defunct
+
+- The `TimeFormat` argument is now deprecated in `SeriesAggreg()`. ([#41](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/41))
+- The `NewTimeFormat` argument is now deprecated in `SeriesAggreg()` and replaced by the `Format` argument. ([#41](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/41))
+- The deprecated `RunSnowModule` argument has been removed from the `CreateRunOptions()` function. ([#23](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/23))
+
+
+#### Bug fixes
+
+- Fixed bug in`SeriesAggreg()`. The function now runs when `TimeLag >= 3600`.
+([#41](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/41))
+- Fixed bug in`SeriesAggreg()`. The function now runs when the time series contain some columns entirely filled with missing values. ([#43](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/43))
+- Fixed bug in `RunModel_GR1A()`. Reversed PotEvap and Precip outputs are now reordered (in the previous versions PotEvap contained the precipitation values and Precip contained the evapotranspiration values, the Qsim values were already correct). ([#65](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/65))
+
+
+#### Major user-visible changes
+
+- Added output to `RunModel_GR2M()` function (Ps). ([#51](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/51))
+- `PE_Oudin()` can now run for several locations (i.e. several latitudes) in the Fortran mode (`RunFortran = TRUE`). In this case `Lat` must be of the same length as `Temp`. ([#62](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/62))
+- `RunModel()` now allows to run semi-distributed GR models. ([#34](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/34))
+- The `ConvertFun` argument of the `SeriesAggreg()` function can now be set to names of aggregation functions that return value of length 1 (not only `"sum"` or `"mean"`, but e.g. `"min"`, `"max"`, `"Q95"`). ([#82](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/82))
+
+
+#### Minor user-visible changes
+
+- The `.FortranOutputs()` function is no longer exported in the namespace.
+- `RunModel_GR1A()` now uses the Fortran version of the model code. This code is no longer duplicated: the R version which was used was removed. ([#65](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/65))
+- Character argument verification now use partial matching in `PE_Oudin()` and `SeriesAggreg()` functions. ([#37](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/37))
+- `RunModel_*()` funcions were cleaned up, with no effect on their outputs. ([#14](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/14))
+- `.ErrorCrit()` function now returns a warning message when a criterion computed on less than 10 time-steps (whatever the unit of the time step). ([#14](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/14))
+- Added the diagram of GR5H in the `RunModel_GR5H()` documentation. ([#49](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/49))
+- The `Exch` was renames `AExch` in the `RunModel_GR2M()` output. ([#87](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/87))
+- Added 'Es' and 'Ps' on the GR2M diagram available in the `RunModel_GR2M()` help page. ([#88](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/88))
+- The `plot.OutputsModel()` function does not check anymore the time step by comparing the calculation of the difference of the last two time steps because it is already checked by the class of the `OutputsModel` object, which is therefore assumed to be necessarily valid. ([#56](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/56))
+
+
+#### Version control and issue tracking
+
+- Implement automatic tests in the package. ([#52](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/52))
+
+
+#### CRAN-compatibility updates
+
+- 'airGR' now depends on R >= 3.1.0 because of the use of the `anyNA` function.
+- The 'hydroPSO' package is back on CRAN and it is again suggested (cf. the 'param_optim' vignette). ([#38](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/38))
+- For more safety, the following "basic" packages are now imported : 'graphics', 'grDevices', 'stats', 'utils. ([#74](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/74))
+
+____________________________________________________________________________________
+
+
+### 1.4.3.65 Release Notes (2020-02-28)
+
+#### CRAN-compatibility updates
+
+- The run period is reduced in the example of the `Imax()` function in order to run faster.
+- The 'hydroPSO' package is no longer suggested (but the code linked to its use and is always present in the 'param_optim' vignette).
+
+____________________________________________________________________________________
+
+
+### 1.4.3.60 Release Notes (2020-01-29)
+
+#### New features
+
+- A digital object identifier (DOI) now allows to identify the manual of the 'airGR' package. When you use 'airGR' in your work, please always cite both the article and the manual. The last one allows to know the version of the package that is used in order to enhance reproducible research. The references can be displayed with the `citation("airGR")` command.
+
+#### Bug fixes
+
+- Fixed bug in `Imax()`. The default value of the `TestedValues` argument was wrong due to a mistyped argument name in the `seq()` function.
+
+____________________________________________________________________________________
+
+
+### 1.4.3.52 Release Notes (2020-01-21)
+
+
+#### New features
+
+- `plot.Outputsmodel()` now allows to draw actual evapotranspiration when `which = "ActEvap"` or `which = "All"` (overlaid to potential evapotranspiration if already drawn). ([#2](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/2))
+- Added `RunModel_GR5H()` and `RunModel_CemaNeigeGR5H()` functions to run the hourly model GR5H (with or without the CemaNeige module). These models present an optional additionnal interception store. ([#13](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/13))
+- Added `Imax()` which allows to estimate the maximum capacity of the GR5H interception store. ([#13](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/13))
+
+
+#### Bug fixes
+
+- Fixed bug in `TransfoParam_GR1A()`. The number of model parameters was wrong (2 instead of 1) which caused an error during the GR1A model calibration. ([#1](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/1))
+- Fixed bug in `plot.OutputsModel()`. The function does not return any error message when `log_scale = TRUE`, `Qobs = NULL` and user want to draw flows time series.
+- Fixed bug in `RunModel_*GR*()`. The functions do not return any error message anymore due to slightly negative values returned by GR4H, GR4J, GR5J or GR6J Fortran codes (the message was returned by `CreateIniStates()` when the final states were created). The `RunModel_*GR*()` functions now return zero instead of these slightly negative values, except for the ExpStore where negatives values are allowed.
+- Fixed bug in the `.ErrorCrit()` function. The Box-Cox transformation formula is now corrected when the `ErrorCrit*()` functions are used.
+
+
+#### Major user-visible changes
+
+- Added outputs to `RunModel_GR4H()` function (Pn, Ps, AExch1, AExch2).
+
+
+#### Minor user-visible changes
+
+- Added the diagram of GR2M in the `RunModel_GR2M()` documentation.
+- Fortran codes cleaned and translated from F77 to F90. ([#18](https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues/18))
+
+
+#### CRAN-compatibility updates
+
+- Cleaning of the Fortran codes (comment formatting).
+
+____________________________________________________________________________________
+
+
+### 1.3.2.42 Release Notes (2019-09-20)
+
+
+#### Version control and issue tracking
+
+- Users can now track changes (`https://gitlab.irstea.fr/HYCAR-Hydro/airgr`) and issues (`https://gitlab.irstea.fr/HYCAR-Hydro/airgr/issues`).
+
+
+#### Bug fixes
+
+- Fixed bug in `RunModel_CemaNeige()`. The function now runs correctly when `IndPeriod_WarmUp = 0L` in `CreateRunOptions()` in order to completely disable the warm-up period (e.g. to perform a forecast form a given initial state).
+- Fixed bug in `CreateIniStates()`. The function now returns the right number of end states when CemaNeige is used without hysteresis.
+- Fixed bug in the `RunModel_CemaNeige*()` functions. G and Gthr end states are no more inverted in the output values.
+
+
+#### Minor user-visible changes
+
+- Spurious flows set to `NA` into the `BasinObs` time series of the `L0123001` dataset.
+
+____________________________________________________________________________________
+
+
+### 1.3.2.23 Release Notes (2019-06-20)
+
+
+#### New features
+
+- `CreateInputsCrit()` now allows power (as a numeric or as a character) and the Box-Cox transformations in the `transfo` argument.
+- Added `RunModel_CemaNeigeGR4H()` function to run the hourly model GR4H with the CemaNeige module.
+- Added `PE_Oudin()` function to compute Oudin's potential evapotranspiration for hourly or daily time steps.
+- `plot.OutputsModel()` now presents a `LayoutMat` argument (and additionnal related argument: `LayoutWidths`, `LayoutHeights`) to specify complex plot arrangements.
+
+
+#### Deprecated and defunct
+
+- The `PEdaily_Oudin()` function is deprecated and his use has been replaced by the use of `PE_Oudin()`.
+
+
+#### Bug fixes
+
+- Fixed bug in `plot.OutputsModel()`. The function now runs correctly when the `which` argument contains the `"CorQQ"` value without `"CumFreq"`.
+
+
+#### Major user-visible changes
+
+- `plot.OutputsModel()` can now draw PE or error time series if the `which` argument is set to `"all"` or `"PotEvap"` or `"Error"`.
+- `plot.OutputsModel()` now allows new values for the which argument: `"all"` corresponds to all graphs, `"synth"` corresponds to the main graphs (default value; corresponding to `"all"` in the previous versions of the package) (i.e. `c("Precip", "Temp", "SnowPack", "Flows", "Regime", "CumFreq", "CorQQ")`), `"ts"` corresponds to the time series graphs (i.e. `c("Precip", "PotEvap", "Temp", "SnowPack", "Flows")`) and "perf" corresponds to the performance graphs (i.e. `c("Error", "Regime", "CumFreq", "CorQQ")`).
+
+
+#### Minor user-visible changes
+
+- `.ErrorCrit()` private function added to check inputs into `ErrorCrit_*()` functions. The `ErrorCrit_*()` functions were simplified accordingly.
+- `CreateInputsCrit()` now returns `FUN_CRIT` as a character string.
+- An example is addeed to illustred the use of the `plot.OutputsModel()` function.
+
+____________________________________________________________________________________
+
+
+### 1.2.13.16 Release Notes (2019-04-03)
+
+
+#### New features
+
+- `CreateInputsCrit()` now presents a `VarObs` argument in order to allow to prepare an `InputsCrit` object in order to run a criterion on other variables than observed discharges with the `ErrorCrit()` function (at the moment SCA and SWE).
+- `CreateInputsCrit()` can now prepare an `InputsCrit` object in order to compute a single criterion (`Single` class), multiple criteria (`Multi` class) or a composite criterion (`Compo` class) with the `ErrorCrit()` function.
+- `CreateInputsCrit()` now presents a `Weights` argument in order to allow to prepare an `InputsCrit` object in order to compute a composite criterion (`Compo` class) with `ErrorCrit()` or `Calibration_Michel()`.
+- `CreateInputsCrit()` now returns a `idLayer` element to indicate which layer(s) to use for SCA or SWE aggregation.
+- `CreateInputsCrit()` now presents a `warnings` argument to replace the verbose action (the `verbose` argument is kept to print messages).
+- In `CreateInputsCrit()`, it is now possible to set the following arguments as atomic (as before) or as list: `FUN_CRIT`, `VarObs`, `Obs`, `BoolCrit`, `transfo`, `Weights`. If the list format is chosen, all the lists must have the same length.
+- `CreateRunOptions()`, `CreateIniStates()` and `CreateCalibOptions()` now present a `IsHyst` argument to give the possibility to use the Linear Hysteresis with CemaNeige. The objects returned present an `hysteresis` class.
+- `CreateRunOptions()` now presents a `warnings` argument to replace the verbose action (the `verbose` argument is kept to print messages).
+- Added `TransfoParam_CemaNeigeHyst()` function in order to take into account transformation of the parameters of the CemaNeige module when the Linear Hysteresis is used.
+- Added the `X0310010` dataset to run the examples using the Linear Hysteresis with CemaNeige (it contains necessary SCA data).
+- Added the 'cemaneige_hysteresis' vignette to explain how to manage the use of the Linear Hysteresis with CemaNeige.
+
+
+#### Deprecated and defunct
+
+- The `Qobs` argument is now deprecated in `CreateInputsCrit()` and has been renamed `Obs`.
+- The `FUN_CRIT` argument is now deprecated in `ErrorCrit()`. This function now gets this information from the `InputsCrit` argument.
+- The `FUN_CRIT` argument is now deprecated in `Calibration_Michel()`. This function now gets this information from the `InputsCrit` argument.
+- The `plot_OutputsModel()` had been deprecated in 'airGR' 1.0.4 (it had been replaced by the use of `plot.OutputsModel()` or `plot()`) and is defunct now.
+
+
+#### Major user-visible changes
+
+- `CreateInputsCrit()` now return a list of `InputsCrit` (each element is of the `Single` class) in the cases of multiple or a composite criteria.
+- `ErrorCrit_*()` functions now return an error message if the `InputsCrit` object is of class `Multi` or `Compo`.
+- `ErrorCrit()` function can now run on a multiple or a composite `InputsCrit`. In these cases, it returns a list of `ErrorCrit`.
+- `ErrorCrit()` and `ErrorCrit_*()` functions can now assess Q, SCA or SWE simulations.
+- `Calibration_Michel()` function can now run on a composite `InputsCrit`. It returns a composite value of error and the formula used to calculate it.
+- Model diagrams added in documentations of `RunModel_GR4J()`, `RunModel_GR5J()` and `RunModel_GR6J()` functions.
+- It is now possible to be redirected to the `plot.OutputsModel()` documentation with `?plot`.
+- It is now possible to use a character vector for all `FUN_*` arguments (in addition to function objects) in the following functions: `Calibration()`, `Calibration_Michel()`, `CreateCalibOptions()`, `CreateIniStates()`, `CreateIniStates()`, `CreateInputsCrit()`, `CreateInputsModel()`, `CreateRunOptions()`, `ErrorCrit()`, `RunModel()` and `TransfoParam()`.
+
+
+#### Minor user-visible changes
+
+- `ErrorCrit_*()` functions now return objects of class `ErrorCrit` and `NSE`, `KGE`, `KGE2` or `RMSE`.
+- `.FortranOutputs()` private function added to manage Fortran outputs.
+- Outputs of `frun_GR2M` Fortran subroutine were reordered.
+- `DataAltiExtrapolation_Valery()` now returns named elements of lists relative to elevation layer.
+- `Calibration()` function now returns an error message if `FUN_CALIB` is not a function.
+- Inputs of `PEdaily_Oudin()` are now checked.
+- `PEdaily_Oudin()` example corrected (the Julian day was one day too early).
+- `plot.OutputsModel()` does not return a warning message anymore when `Qobs = NULL`.
+- Inputs of `TransfoParam*()` functions are now checked.
+- The order of authors has been updated in the DESCRIPTION and the CITATION files.
+
+
+#### CRAN-compatibility updates
+
+- Tabulations removed, unused variables removed and variable statements fixed in Fortran files.
+
+____________________________________________________________________________________
+
+
+### 1.0.15.2 Release Notes (2018-10-10)
+
+
+#### Bug fixes
+
+- Fixed bug in `CreateRunOptions()`. The function now accounts correctly for leap years when no warm-up period is defined.
+
+
+#### Minor user-visible changes
+
+- `CreateRunOptions()` was cleaned up, with no effect on its outputs.
+
+
+#### CRAN-compatibility updates
+
+- The `vignetteParam*.rda` datasets moved to the inst directory. It contains different objects needed for 'param_optim' and 'param_mcmc' vignettes.
+
+____________________________________________________________________________________
+
+
+### 1.0.14.1 Release Notes (2018-09-28)
+
+
+#### New features
+
+- `PEdaily_Oudin()` now presents a `LatUnit` argument which allows to choose the unit of the latitude (radians and degrees).
+
+
+#### Deprecated and defunct
+
+- The `LatRad` argument is now deprecated in `PEdaily_Oudin()` and replaced by the `Lat` argument.
+- The unused `Ind_zeroes` argument of the `CreateInputsCrit()` function is now deprecated.
+- The `verbose` argument is now deprecated in `CreateInputsCrit()` and replaced by the `warnings` argument.
+
+
+#### Major user-visible changes
+
+- `Calibration_Michel()` is now faster during the grid-screening step when a parameter is set using `FixedParam` in `CreateCalibOptions()`.
+- `CreateCalibOptions()` now returns an error when all the parameters are set in the `FixedParam` argument and a warning message when all the parameters are free (NA) in the `FixedParam` argument.
+- `CreateInputsCrit()` now returns an error when `epsilon` is not positive.
+- `CreateInputsCrit()` now returns a warning message in the following case: there are zeroes values in `Qobs`, `epsilon = NULL` and `transfo = log` or `inv`.
+- `ErrorCrit_*()` functions now return a warning message in the following case: there are zeroes values in `Qobs` or `Qsim`, `epsilon = NULL` and `transfo = log` or `inv`.
+
+
+#### Minor user-visible changes
+
+- Several functions of the package were cleaned up or slightly modified, with no effect on their outputs.
+- Dubious Qls and Qmm values set to NA values between 1997-01-05 and 1997-01-21 in the `L0123001` dataset.
+- ORCID numbers are now joined to the names of the authors of the package.
+
+
+#### CRAN-compatibility updates
+
+- Function name changed in a vignettes to avoid error during the check on Debian distribution
+- As recomanded by CRAN managers, the NEWS file is now at the text format and is no more just a link to the 'airGR' Website
+- Added the `Vignette_Param.` datasets in order to reduce runtime during the re-building of vignettes. It contains different objects needed for param_optim and param_mcmc vignettes.
+
+____________________________________________________________________________________
+
+
+### 1.0.10.11 Release Notes (2018-06-29)
+
+
+#### Bug fixes
+
+- Fixed bug in `RunModel_GR2M()`. The function now returns the total precipitation (P) instead of the net rainfall (P1).
+
+
+#### Major user-visible changes
+
+- `RunModel_GR2M()` now returns more explicit precipitation outputs names.
+- `CreateInputsCrit()` now returns a warning message when the KGE (or KGE') is used with a log transformation on flows.
+- The article reference is corrected.
+
+
+#### Minor user-visible changes
+
+- The documentation and help of several functions were improved.
+
+____________________________________________________________________________________
+
+
+### 1.0.9.64 Release Notes (2017-11-10)
+
+
+#### New features
+
+- An article describing the 'airGR' package has been published. Its reference has been added and will be displayed with `citation("airGR")`.
+- Added `CreateIniStates()` function in order to help user to format the `IniStates` argument for `CreateRunOptions()`.
+- Added the `Param_Sets_GR4J` dataset. It contains generalist parameter sets for the GR4J model.
+- Three vignettes have been added. They are relative to different calibration methods (including the generalist parameters sets of the GR4J model).
+
+
+#### Deprecated and defunct
+
+- The `RunSnowModule` argument is now deprecated in `CreateRunOptions()`.
+
+
+#### Bug fixes
+
+- Fixed bug in `RunModel_GR4H()`: in `frun_GR4H` Fortran subroutine, `St(2)` is now set to 0 (instead of `St(1)`) when `St(2) < 0`.
+- Fixed bug in `plot.OutputsModel()` for the regime plot when the period is less than 1 year.
+- Fixed bug in `plot.OutputsModel()` when there is no common data to plot the cumulative frequency or the correlation QQ.
+- Fixed bug in `plot.OutputsModel()` for the y-axis labelling of flows time series when `log_scale = TRUE` and `BasinArea` is used.
+
+
+#### Major user-visible changes
+
+- `RunModel_GR4J()`, `RunModel_GR5J()` and `RunModel_GR6J()` (and `CemaNeige_GR*J()`) now return Ps, Pn and actual exchanges. See the model Fortran codes for more details about the calculation of these variables.
+- `CreateInputsModel()` now returns an error when `DatesR` contains duplicated values.
+- `RunModel_GR5J` now returns `StateEnd` in the same order as the other models.
+
+
+#### Minor user-visible changes
+
+- `plot.OutputsModel()` now returns a warning message when the length of Qobs is different from the length of Qsim.
+- The X1 parameter from GR4H, GR4J, GR2M, GR5J and GR6J, the X3 parameter from GR4H, GR4J, GR5J and GR6J and the X6 parameter from GR6J are now set to 1e-2 when they are fixed to lower values. `RunModel_*()` functions now return a warning message in this case. `RunModel_*()` functions now return a warning when X4 < 0.5 and its value is set to 0.5.
+- The commands `?L0123001`, `?L0123002` and `?L0123003` now return the documentation page related to `BasinObs`.
+- Many functions of the package were cleaned up or slightly modified, with no effect on their outputs.
+- The documentation and help of several functions were improved.
+
+
+#### CRAN-compatibility updates
+
+- "airGR.c" file registers native routines.
+
+____________________________________________________________________________________
+
+
+### 1.0.5.12 Release Notes (2017-01-23)
+
+
+#### New features
+
+- `DataAltiExtrapolation_Valery()` and `CreateInputsModel()` now present a `PrecipScale` argument which allows rescaling precipitation when it is interpolated on the elevation layers when CemaNeige is used.
+
+
+#### Bug fixes
+
+- Fixed bug in `DataAltiExtrapolation_Valery()`. The elevation gradients for air temperature returned by `CreateInputsModel()` are improved.
+
+
+#### User-visible changes
+
+- `DataAltiExtrapolation_Valery()` has been improved. `DataAltiExtrapolation_Valery()` now runs faster (and by consequence `CreateInputsModel()` too, when CemaNeige is used).
+
+____________________________________________________________________________________
+
+
+### 1.0.4 Release Notes (2017-01-18)
+
+
+#### New features
+
+- `RunModel_CemaNeige()`, `RunModel_CemaNeigeGR4J()`, `RunModel_CemaNeigeGR5J()` and `RunModel_CemaNeigeGR6J()` now return air temperature for each elevation layer.
+
+
+#### Deprecated and defunct
+
+- S3 plot method defined for `OutputsModel` objects. It means that the `plot_OutputsModel()` function is deprecated and his use has been replaced by the use of `plot.OutputsModel()` or `plot()`.
+- In `plot.OutputsModel()` the `PlotChoice` argument is deprecated and has been renamed `which`.
+
+
+#### User-visible changes
+
+- `plot.OutputsModel()` displays air temperature time series for each layer when `CemaNeige` is used (argument `which = "Temp"` or `"all"`).
+
+____________________________________________________________________________________
+
+
+### 1.0.3 Release Notes (2016-12-09)
+
+
+#### New features
+
+- `ErrorCrit_*()` functions gain a `warnings` argument to replace the verbose action and the `verbose` argument now prints the criterion value(s).
+
+
+#### Bug fixes
+
+- Fixed bug in `CreateCalibOptions()` when `StartParamList` or `StartParamDistrib` arguments are used.
+
+
+#### User-visible changes
+
+- `CreateInputsModel()` now returns an error if `NLayers <= 0` when `CemaNeige` is used.
+- `plot_OutputsModel()` now displays raw values on the y-axis when the discharge time series is represented with log scale (formerly, log values of discharges were displayed on the y-axis).
+
+____________________________________________________________________________________
+
+
+### 1.0.2 Release Notes (2016-11-03)
+
+
+#### New features
+
+- `SeriesAggreg()` gains a `TimeLag` argument that corresponds to a numeric value indicating a time lag (in seconds) for the time series aggregation (useful to aggregate hourly time series to the daily time step for instance).
+ In addition, the function now accepts input dates in both `POSIXt` formats (`POSIXct` and `POSIXlt`). The output is in `POSIXct` format.
+- `plot_OutputsModel()` gains a `log_scale` argument in order to plot the flow with a log scale.
+- A tutorial is available online on the following link: https://hydrogr.github.io/airGR/.
+ It can also be displayed with the `vignette("airGR")` command.
+
+
+#### Deprecated and defunct
+
+- `CreateCalibOptions()` loses the `OptimParam` argument that was redundant with the `FixedParam` argument. The `Calibration_Michel()` was modified to take into account this change by using directly `FixedParam`, but this is transparent to the user.
+- `CreateCalibOptions()` loses the `StartParam` argument that was not used.
+
+
+#### Bug fixes
+
+- The value `sort` for the `transfo` argument of `CreateInputsCrit()` was not taken into account. It is now fixed.
+
+
+#### Major user-visible changes
+
+- The `RunModel_GR6J()` and `RunModel_CemaNeigeGR6J()` models were modified back to versions previous to 1.0.1 to prevent from unwanted efficiency criteria deterioration related to the calibration with `Calibration_Michel()`.
+ The actual model codes were not modified but the `TransfoParam_GR6J()` and `CreateCalibOptions()` functions were modified regarding the X5 parameter.
+ It is strongly advised to use airGR 1.0.2 for the `RunModel_GR6J()` and `RunModel_CemaNeigeGR6J()` functions if you are using `Calibration_Michel()`, as they are much more efficient.
+ In case you were using your own calibration algorithm, you will not notice any difference.
+
+
+#### Minor user-visible changes
+
+- `CreateInputsModel()` and `DataAltiExtrapolation_Valery()` functions now allow both `POSIXt` formats (`POSIXct` and `POSIXlt`).
+
+____________________________________________________________________________________
+
+
+### 1.0.1 Release Notes (2016-04-21)
+
+
+#### Deprecated and defunct
+
+- The `Calibration_HBAN()` and `DataAltiExtrapolation_HBAN()` functions have respectively been renamed as `Calibration_Michel()` and `DataAltiExtrapolation_Valery()` after the names of their creators.
+- The `Calibration_optim()` function has been removed from the package.
+- The silent mode is now defined by the `verbose = TRUE` argument (formerly `quiet = FALSE`) in the following functions:
+`Calibration()`, `Calibration_Michel()`, `CreateInputsModel()`, `CreateRunOptions()`, `DataAltiExtrapolation_Valery()`, `ErrorCrit()`, `ErrorCrit_KGE()`, `ErrorCrit_KGE2()`, `ErrorCrit_NSE()`, `ErrorCrit_RMSE()`, `plot_OutputsModel()`, `SeriesAggreg()`.
+
+
+#### Major user-visible changes
+- The GR5J model has been modified: previously, two unit hydrographs were used, now only one is remaining.
+ As a consequence, simulations from the GR5J (`RunModel_GR5J()` function) and CemaNeige (`RunModel_CemaNeigeGR5J()` function) models will be different.
+- An important proportion of the transformations of the parameters have been modified (`TransfoParam_*()` functions). Since this modifies the local search, calibration results will be different .
+- The quantiles of the parameters have been recalculated with the new transformations (`CreateCalibOptions()` function). Since these quantiles constitute the starting point of the calibration algorithm, calibration results will be different.
+
+
+#### Minor user-visible changes
+
+- The Fortran model core codes have been modified:
+	- optimisation of the codes for fastening of computation;
+	- simplification of the internal variables for easier reading and understanding.
+- The list of the contributors and authors is now full.
+- The references of the package has been updated; they are returned by the following R-command `citation("airGR")`.
+
+____________________________________________________________________________________
+
+
+### 0.8.1.2 Release Notes (2015-08-21)
+
+
+#### Bug fixes
+
+- Fixed bug in `CreateInputsModel()` that was related to the handling of missing values.
+- Fixed bug in `CreateRunOptions()` that prevented the correct use of the `IniResLevels` argument (to manually set the filling rate of the production and routing stores).
+
+
+#### Minor user-visible changes
+
+- Removal of an unnecessary warning when `IndPeriod_WarmUp = 0`.
+
+
+#### CRAN-compatibility updates
+
+- Modification of namespace file to ensure proper use under linux without compilation issues.
+
+____________________________________________________________________________________
+
+
+### 0.8.0.2 Release Notes (2015-04-15)
+
+
+#### New features
+
+- Three new hydrological models: `RunModel_GR4H() function for ` GR4H (hourly), `RunModel_GR2M()` function for GR2M (monthly) and `RunModel_GR1A()` function for GR1A (yearly).
+- New function `SeriesAggreg()` to easily aggreg timesteps.
+
+
+#### Bug fixes
+
+- Fixed bug in `ErrorCrit_RMSE()` which led to incorrect calibration (the criterion was maximised instead of minimised).
+
+
+#### Major user-visible changes
+
+- Update of the functions `CreateRunOptions()`, `CreateCalibOptions()` and `plot_OutputsModel()` to handle the new models.
+- Modification of CemaNeige Fortran code to add an update of Gratio after the SnowPack update (no impact on snow simulation).
+
+
+#### Minor user-visible changes
+
+- Improvement of the `plot_OutputsModel()` function to allow a selection among available plots.
+- Minor update in `ErrorCrit_KGE()` and `ErrorCrit_KGE2()` to handle case when only one values in not NA.
+- Update of the scripts in airGR-advanced-example to match the structures of the `BasinData` objects.
+- Correction of formatting issue in airGR-advanced-example regarding the "List_HypsoData.txt" file.
+
+____________________________________________________________________________________
+
+
+### 0.7.4 Release Notes (2014-11-01)
+
+
+#### New features
+
+- New argument in many functions (`quiet = TRUE` or `FALSE`) to choose if the warnings should be suppressed or not.
+
+
+#### Deprecated and defunct
+
+- The `CalibrationAlgo_*()` functions were renamed into `Calibration_*()`.
+
+
+#### Bug fixes
+
+- Fixed bug in `CreateCalibOptions()` to handle models with only one parameter.
+- Fixed bug in `Calibration_HBAN()`. The function was not working properly with models having only one parameter.
+
+
+#### Major user-visible changes
+
+- CemaNeige users must now specify one `MeanAnSolidPrecip` for each elevation layer. The `CreateRunOptions()` function is impacted.
+- CemaNeige users can now specify the mean elevation of the input series (before it was always considered equal to the catchment median elevation).
+ The impacted functions are `CreateInputsModel()` and `DataAltiExtrapolation_HBAN()`.
+- New architecture with better format verification procedure (using classes) and simpler setting of default configuration.
+- New architecture where the model, calibration and error functions are in the arguments of the functions
+ (the exotic use of "generic function" created by the users has been removed).
+- Improved documentation and examples.
+
+
+#### Minor user-visible changes
+
+- Improvements allowing the arrival of new models.
+- Improvements of the argument verifications in `CreateInputsModel()`, `CreateRunOptions()`, `CreateInputsCrit()`, `CreateCalibOptions()`.
+- Improvements of all the `ErrorCrit()` functions to better account for the cases with constant flow values or local zeros.
+- Improvement of the `plot_OutputsModel` function (to handle 0 in Qobs and Qsim).
+- Improved documentation.
+
+____________________________________________________________________________________
+
+
+### 0.6.2 Release Notes (2014-02-12)
+
+
+#### New features
+
+- Additional functions for results plotting (the 'zoo' package is required for some of them).
+- Add multi-objective calibration using `nsga2()` (the 'mco' package is required).
+- The field Multiplier has been added in the ErrorCrit() outputs, to indicate whether the criterion is an error (to minimise) or and efficiency (to maximise).
+ This allows to provide real efficiency values in the outputs e.g. NSE[Q] instead of (-1) &times; NSE[Q].
+
+
+#### Deprecated and defunct
+
+- `EfficiencyCrit()` have been replaced by `ErrorCrit()` to avoid misunderstanding (by default, the algorithms minimise the error criterion).
+
+
+#### Bug fixes
+
+- RC11 bug correction: the automatic selection of the warm-up period was not working properly when no data was available from warm-up (i.e. when the user had set the run to start at the very first index).
+- RC10 bug correction: the `CalibrationAlgo_HBAN()` function was not working in the very rare case when the diagonal search was activated and lead to a set outside the authorised range.
+- RC9 bug correction: the `CalibrationAlgo_HBAN()` function was not working properly with models having only one parameter.
+- RC8 bug correction of the `ModelDefaultIniOptions()` function (this bug was introduced in the RC7 and caused an error when `IndPeriod_WarmUp = NULL`.
+- RC7 bug correction of the `ModelDefaultIniOptions()` function (the automatic selection of one year for warm-up was not handling properly missing data).
+- RC6 correction of the help files (the description of CemaNeige parameters were inverted).
+- RC5 differs from previous releases in the way the data are read and stored (in a list instead of individual vectors).
+ The package is similar, only the examples of Main and the files in MyScriptBlocks have changed.
+ All basin data are now stored inside a list named `BasinData`. This will greatly ease the future use of Rdata files (instead of txt files) as storage format for the time series of observation.
+
+
+#### Major user-visible changes
+
+- The definition of the generic function is now made in a much simpler way (e.g. see `DefineFunctions_Model()` or `DefineFunctions_ErrorCrit()`).
+
+
+#### Minor user-visible changes
+
+- Code improvements to reduce the computation time.
+- Clearer instructions for the adding and modification of a model.
+- Improvements of the documentation.
+
+
+____________________________________________________________________________________
+
+
+### 0.5.2 Release Notes (2014-02-05)
+
+
+#### Deprecated and defunct
+
+- The `SelectPer` arguments are replaced by `IndPeriod` to ease understanding.
+- The `PE` arguments are replaced by `PotEvap()` to ease understanding.
+- The `Fsol` arguments are replaced by `FracSolidPrecip` to ease understanding.
+
+
+#### Major user-visible changes
+
+- R <= 2.15 in not supported by default.
+- The check that `SelectPer_Run()` is continuous is now made in the `CheckArg()` functions.
+- Check of the model functioning time step.
+- Name of the calibration criterion provided in `OutputsAlgo()`.
+
+
+#### Minor user-visible changes
+
+- Missing values in Fortran are now -999.999 instead of -9.999.
+
+
+____________________________________________________________________________________
+
+
+### 0.5.1 Release Notes (2014-01-27)
+
+
+#### New features
+
+- New `EfficiencyCrit_NSE_sqrtQ()` function to compute NSE criterion on sqrt flows.
+
+
+#### Bug fixes
+
+- Incorrect arguments in the call to `RunModelAndCrit` from `CalibrationAlgo_optim_stats` and `CalibrationAlgo_nlminb_stats`.
+- `CalibrationAlgo_nlminb_stats` argument was wrongly defined in `DefineFunctions_CalibrationAlgo()` (`optim` instead of `nlminb`).
+- Format checking for `RunOptions` was incorrectly made in `CheckArg()` function.

NEWS.rmd

----
-title: "Release History of the airGR Package"
-output: 
-  html_document:
-    toc: true
-    toc_float: true
-    depth: 3  # upto three depths of headings (specified by #, ### and ###)
-    number_sections: false  ### if you want number sections at each table header
-    theme: united  # many options for theme, this one is my favorite.
-    highlight: tango  # specifies the syntax highlighting style  
-    keep_md: true
----
-
-
-
-### 1.0.15.3 Release Notes (2018-10-15) 
-
-
-
-
-____________________________________________________________________________________
-
-
-### 1.0.15.2 Release Notes (2018-10-10) 
-
-
-#### Bug fixes
-
-- Fixed bug in <code>CreateRunOptions()</code>. The function now accounts correctly for leap years when no warm-up period is defined.
-
-
-#### Minor user-visible changes
-
-- <code>CreateRunOptions()</code> was cleant, with no effect on its outputs.
-
-
-#### CRAN-compatibility updates
-
-- The <code>Vignette_Param.</code> datasets moved to the inst directory. It contains different objects needed for param_optim and param_mcmc vignettes.
-
-____________________________________________________________________________________
-
-
-### 1.0.14.1 Release Notes (2018-09-28) 
-
-
-#### Deprecated and defunct
-
-- The <code>LatRad</code> argument is now deprecated in <code>PEdaily_Oudin()</code> and replaced by the <code>Lat</code> argument.
-
-- The unused <code>Ind_zeroes</code> argument of the <code>CreateInputsCrit()</code> function is now deprecated.
-
-
-#### New features
-
-- <code>PEdaily_Oudin()</code> now presents a <code>LatUnit</code> argument which allows to choose the unit of the latitude (radians and degrees).
-
-
-#### Major user-visible changes
-
-- <code>Calibration_Michel()</code> is now faster during the grid-screening step when a parameter is set using <code>FixedParam</code> in <code>CreateCalibOptions()</code>.
-
-- <code>CreateCalibOptions()</code> now returns an error when all the parameters are set in the <code>FixedParam</code> argument and a warning message when all the parameters are free (NA) in the <code>FixedParam</code> argument.
-
-- <code>CreateInputsCrit()</code> now returns an error when <code>epsilon</code> is not positive.
-
-- <code>CreateInputsCrit()</code> now returns a warning message in the following case: there are zeroes values in <code>Qobs</code>, <code>epsilon = NULL</code> and <code>transfo = log</code> or <code>inv</code>.
-
-- <code>ErrorCrit*()</code> functions now return a warning message in the following case: there are zeroes values in <code>Qobs</code> or <code>Qsim</code>, <code>epsilon = NULL</code> and <code>transfo = log</code> or <code>inv</code>.
-
-
-#### Minor user-visible changes
-
-- Several functions of the package were cleant or slightly modified, with no effect on their outputs.
-
-- Dubious Qls and Qmm values set to NA values between 1997-01-05 and 1997-01-21 in the L0123001 dataset.
-
-- ORCID numbers are now joined to the names of the authors of the package.
-
-
-#### CRAN-compatibility updates
-
-- Function name changed in a vignettes to avoid error during the check on Debian distribution
-
-- As recomanded by CRAN managers, the NEWS file is now at the text format and is no more just a link to the airGR Website
-
-- Added the <code>Vignette_Param.</code> datasets in order to reduce runtime during the re-building of vignettes. It contains different objects needed for param_optim and param_mcmc vignettes.
-
-____________________________________________________________________________________
-
-
-### 1.0.10.11 Release Notes (2018-06-29) 
-
-
-#### Bug fixes
-
-- Fixed bug in <code>RunModel_GR2M()</code>. The function now returns the total precipitation (P) instead of the net rainfall (P1).
-
-
-#### Major user-visible changes
-
-- <code>RunModel_GR2M()</code> now returns more explicit precipitation outputs names.
-
-- <code>CreateInputsCrit()</code> now returns a warning message when the KGE (or KGE') is used with a log transformation on flows.
-
-- The article reference is corrected.
-
-
-#### Minor user-visible changes
-
-- The documentation and help of several functions were improved.
-
-____________________________________________________________________________________
-
-
-### 1.0.9.64 Release Notes (2017-11-10) 
-
-
-#### New features
-
-- An article describing the airGR package has been published. Its reference has been added and will be displayed with <code>citation("airGR")</code>. 
-
-- Added <code>CreateIniStates()</code> function in order to help user to format the <code>IniStates</code> argument for <code>CreateRunOptions()</code>.
-
-- Added the <code>Param_Sets_GR4J</code> dataset. It contains generalist parameter sets for the GR4J model.
-
-- Three vignettes have been added. They are relative to different calibration methods (including the generalist parameters sets of the GR4J model).
-
-
-#### Bug fixes
-
-- Fixed bug in <code>RunModel_GR4H()</code>: in <code>frun_GR4H</code> Fortran subroutine, <code>St(2)</code> is now set to 0 (instead of <code>St(1)</code>) when <code>St(2) < 0</code>. 
-
-- Fixed bug in <code>plot.OutputsModel()</code> for the regime plot when the period is less than 1 year.
-
-- Fixed bug in <code>plot.OutputsModel()</code> when there is no common data to plot the cumulative frequency or the correlation QQ.
-
-- Fixed bug in <code>plot.OutputsModel()</code> for the y-axis labelling of flows time series when <code>log_scale = TRUE</code> and <code>BasinArea</code> is used.
-
-
-#### Deprecated and defunct
-
-- The <code>RunSnowModule</code> argument is now deprecated in <code>CreateRunOptions()</code>.
-
-
-#### Major user-visible changes
-
-- <code>RunModel_GR4J()</code>, <code>RunModel_GR5J()</code> and <code>RunModel_GR6J()</code> (and <code>CemaNeige_GR&#42;J()</code>) now return Ps, Pn and actual exchanges. See the model Fortran codes for more details about the calculation of these variables.
-
-- <code>CreateInputsModel()</code> now returns an error when <code>DatesR</code> contains duplicated values.
-
-- <code>RunModel_GR5J</code> now returns <code>StateEnd</code> in the same order as the other models.
-
-
-#### Minor user-visible changes
-
-- <code>plot.OutputsModel()</code> now returns a warning message when the length of Qobs is different from the length of Qsim. 
-
-- The X1 parameter from GR4H, GR4J, GR2M, GR5J and GR6J, the X3 parameter from GR4H, GR4J, GR5J and GR6J and the X6 parameter from GR6J are now set to 1e-2 when they are fixed to lower values. <code>RunModel&#42;()</code> functions now return a warning message in this case. <code>RunModel&#42;()</code> functions now return a warning when X4 < 0.5 and its value is set to 0.5.
-
-- The commands <code>?L0123001</code>, <code>?L0123002</code> and <code>?L0123003</code> now return the documentation page related to <code>BasinObs</code>.
-
-- Many functions of the package were cleant or slightly modified, with no effect on their outputs. 
-
-- The documentation and help of several functions were improved.
-
-
-#### CRAN-compatibility updates
-
-- "airGR.c" file registers native routines.
-
-____________________________________________________________________________________
-
-
-### 1.0.5.12 Release Notes (2017-01-23) 
-
-
-#### New features
-
-- <code>DataAltiExtrapolation_Valery()</code> and <code>CreateInputsModel()</code> now present a <code>PrecipScale</code> argument which allows rescaling precipitation when it is interpolated on the elevation layers when CemaNeige is used.
-
-
-#### Bug fixes
-
-- Fixed bug in <code>DataAltiExtrapolation_Valery()</code>. The elevation gradients for air temperature returned by <code>CreateInputsModel()</code> are improved.
-
-
-#### User-visible changes
-
-- <code>DataAltiExtrapolation_Valery()</code> has been improved. <code>DataAltiExtrapolation_Valery()</code> now runs faster (and by consequence <code>CreateInputsModel()</code> too, when CemaNeige is used).
-
-____________________________________________________________________________________
-
-
-### 1.0.4 Release Notes (2017-01-18) 
-
-#### New features
-
-- <code>RunModel_CemaNeige()</code>, <code>RunModel_CemaNeigeGR4J()</code>, <code>RunModel_CemaNeigeGR5J()</code> and <code>RunModel_CemaNeigeGR6J()</code> now return air temperature for each elevation layer. 
-
-
-#### Deprecated and defunct
-
-- S3 plot method defined for <code>OutputsModel</code> objects. It means that the <code>plot_OutputsModel()</code> function is deprecated and his use has been replaced by the use of <code>plot.OutputsModel()</code> or <code>plot()</code>.
-
-- In <code>plot.OutputsModel()</code> the <code>PlotChoice</code> argument is deprecated and has been renamed <code>which</code>.
-
-
-#### User-visible changes
-
-- <code>plot.OutputsModel()</code> displays air temperature time series for each layer when <code>CemaNeige</code> is used (argument <code>which = "Temp"</code> or <code>"all"</code>).
-
-____________________________________________________________________________________
-
-
-### 1.0.3 Release Notes (2016-12-09) 
-
-#### New features
-
-- <code>ErrorCrit&#42;()</code> functions gain a warnings argument to replace the verbose action and the verbose argument now prints the criterion value(s).
-
-
-#### Bug fixes
-
-- Fixed bug in <code>CreateCalibOptions()</code> when <code>StartParamList</code> or <code>StartParamDistrib</code> arguments are used.
-
-
-#### User-visible changes
-
-- <code>CreateInputsModel()</code> now returns an error if <code>NLayers <= 0</code> when <code>CemaNeige</code> is used.
-
-- <code>plot_OutputsModel()</code> now displays raw values on the y-axis when the discharge time series is represented with log scale (formerly, log values of discharges were displayed on the y-axis).
-
-
-____________________________________________________________________________________
-
-
-### 1.0.2 Release Notes (2016-11-03) 
-
-
-#### New features
-
-- <code>SeriesAggreg()</code> gains a TimeLag argument that corresponds to a numeric value indicating a time lag (in seconds) for the time series aggregation (useful to aggregate hourly time series to the daily time step for instance).
- In addition, the function now accepts input dates in both POSIXt formats (POSIXct and POSIXlt). The output is in POSIXct format.
- 
-- <code>plot_OutputsModel()</code> gains a <code>log_scale</code> argument in order to plot the flow with a log scale.
-
-- A tutorial is available online on the following link: from http://webgr.irstea.fr/airGR.
- It can also be displayed with the <code>vignette("airGR")</code> command.
- 
-
-#### Bug fixes
-
-- The value <code>sort</code> for the <code>transfo</code> argument of <code>CreateInputsCrit()</code> was not taken into account. It is now fixed. 
-
-
-#### Deprecated and defunct
-
-- <code>CreateCalibOptions()</code> loses the OptimParam argument that was redundant with the <code>FixedParam</code> argument. The <code>Calibration_Michel()</code> was modified to take into account this change by using directly <code>FixedParam</code>, but this is transparent to the user. 
-
-- <code>CreateCalibOptions()</code> loses the StartParam argument that was not used. 
-
- 
-#### Major user-visible changes
-
-- The <code>RunModel_GR6J()</code> and <code>RunModel_CemaNeigeGR6J()</code> models were modified back to versions previous to 1.0.1 to prevent from unwanted efficiency criteria deterioration related to the calibration with <code>Calibration_Michel()</code>. 
- The actual model codes were not modified but the <code>TransfoParam_GR6J()</code> and <code>CreateCalibOptions()</code> functions were modified regarding the X5 parameter. 
- It is strongly advised to use airGR 1.0.2 for the <code>RunModel_GR6J()</code> and <code>RunModel_CemaNeigeGR6J()</code> functions if you are using <code>Calibration_Michel()</code>, as they are much more efficient. 
- In case you were using your own calibration algorithm, you will not notice any difference. 
-
-
-#### Minor user-visible changes
-
-- <code>CreateInputsModel()</code> and <code>DataAltiExtrapolation_Valery()</code> functions now allow both POSIXt formats (POSIXct and POSIXlt).
-
-
-____________________________________________________________________________________
-
-
-### 1.0.1 Release Notes (2016-04-21) 
-
-#### Deprecated and defunct
-
-- The <code>Calibration_HBAN()</code> and <code>DataAltiExtrapolation_HBAN()</code> functions have respectively been renamed as <code>Calibration_Michel()</code> and <code>DataAltiExtrapolation_Valery()</code> after the names of their creators.
-
-- The <code>Calibration_optim()</code> function has been removed from the package.
-
-- The silent mode is now defined by the <code>verbose = TRUE</code> argument (formerly <code>quiet = FALSE</code>) in the following functions:
-<code>Calibration()</code>, <code>Calibration_Michel()</code>, <code>CreateInputsModel()</code>, <code>CreateRunOptions()</code>, <code>DataAltiExtrapolation_Valery()</code>, <code>ErrorCrit()</code>, <code>ErrorCrit_KGE()</code>, <code>ErrorCrit_KGE2()</code>, <code>ErrorCrit_NSE()</code>, <code>ErrorCrit_RMSE()</code>, <code>plot_OutputsModel()</code>, <code>SeriesAggreg()</code>.
-
-
-#### Major user-visible changes
-- The GR5J model has been modified: previously, two unit hydrographs were used, now only one is remaining.
- As a consequence, simulations from the GR5J (<code>RunModel_GR5J()</code> function) and CemaNeige (<code>RunModel_CemaNeigeGR5J()</code> function) models will be different.
-
-- An important proportion of the transformations of the parameters have been modified (<code>TransfoParam&#42;()</code> functions). Since this modifies the local search, calibration results will be different .
-
-- The quantiles of the parameters have been recalculated with the new transformations (<code>CreateCalibOptions()</code> function). Since these quantiles constitute the starting point of the calibration algorithm, calibration results will be different.
-
-
-#### Minor user-visible changes
-
-- The Fortran model core codes have been modified:
-	- optimisation of the codes for fastening of computation;
-	- simplification of the internal variables for easier reading and understanding.
-	
-- The list of the contributors and authors is now full.
-
-- The references of the package has been updated; they are returned by the following R-command <code>citation("airGR")</code>.
-
-____________________________________________________________________________________
-
-
-### 0.8.1.2 Release Notes (2015-08-21) 
-
-#### Bug fixes
-
-- Fixed bug in <code>CreateInputsModel()</code> that was related to the handling of missing values.
-
-- Fixed bug in <code>CreateRunOptions()</code> that prevented the correct use of the <code>IniResLevels</code> argument (to manually set the filling rate of the production and routing stores).
-
-
-#### Minor user-visible changes
-
-- Removal of an unnecessary warning when <code>IndPeriod_WarmUp = 0</code>.
-
-
-#### CRAN-compatibility updates
-
-- Modification of namespace file to ensure proper use under linux whithout compilation issues.
-
-
-____________________________________________________________________________________
-
-
-### 0.8.0.2 Release Notes (2015-04-15) 
-
-
-#### New features
-
-- Three new hydrological models: <code>RunModel_GR4H() function for </code> GR4H (hourly), <code>RunModel_GR2M()</code> function for GR2M (monthly) and <code>RunModel_GR1A()</code> function for GR1A (yearly).
-
-- New function <code>SeriesAggreg()</code> to easily aggreg timesteps.
-
-
-#### Bug fixes
-
-- Fixed bug in <code>ErrorCrit_RMSE()</code> which led to incorrect calibration (the criterion was maximised instead of minimised).
-
-
-#### Major user-visible changes
-
-- Update of the functions <code>CreateRunOptions()</code>, <code>CreateCalibOptions()</code> and <code>plot_OutputsModel()</code> to handle the new models.
-
-- Modification of CemaNeige Fortran code to add an update of Gratio after the SnowPack update (no impact on snow simulation).
-
-
-#### Minor user-visible changes
-
-- Improvement of the <code>plot_OutputsModel()</code> function to allow a selection among available plots.
-
-- Minor update in <code>ErrorCrit_KGE()</code> and <code>ErrorCrit_KGE2()</code> to handle case when only one values in not NA.
-
-- Update of the scripts in airGR-advanced-example to match the structures of the <code>BasinData</code> objects.
-
-- Correction of formatting issue in airGR-advanced-example regarding the "List_HypsoData.txt" file.
-
-
-____________________________________________________________________________________
-
-
-### 0.7.4 Release Notes (2014-11-01) 
-
-
-#### New features
-
-- New argument in many functions (<code>quiet = TRUE</code> or <code>FALSE</code>) to choose if the warnings should be suppressed or not.
-
-
-#### Bug fixes
-
-- Fixed bug in <code>CreateCalibOptions()</code> to handle models with only one parameter.
-
-- Fixed bug in <code>Calibration_HBAN()</code>. The function was not working properly with models having only one parameter.
-
-
-#### Deprecated and defunct
-
-- The <code>CalibrationAlgo_&#42;()</code> functions were renamed into<code>Calibration_&#42;()</code>.
-
-
-#### Major user-visible changes
-
-- CemaNeige users must now specify one <code>MeanAnSolidPrecip</code> for each elevation layer. The <code>CreateRunOptions()</code> function is impacted.
-
-- CemaNeige users can now specify the mean elevation of the input series (before it was always considered equal to the catchment median elevation). 
- The impacted functions are <code>CreateInputsModel()</code> and <code>DataAltiExtrapolation_HBAN()</code>.
- 
-- New architecture with better format verification procedure (using classes) and simpler setting of default configuration.
-
-- New architecture where the model, calibration and error functions are in the arguments of the functions
- (the exotic use of "generic function" created by the users has been removed).
-
-- Improved documentation and examples. 
-
-
-#### Minor user-visible changes
-
-- Improvements allowing the arrival of new models.
-
-- Improvements of the argument verifications in <code>CreateInputsModel()</code>, <code>CreateRunOptions()</code>, <code>CreateInputsCrit()</code>, <code>CreateCalibOptions()</code>.
-
-- Improvements of all the <code>ErrorCrit()</code> functions to better account for the cases with constant flow values or local zeros.
-
-- Improvement of the <code>plot_OutputsModel</code> function (to handle 0 in Qobs and Qsim).
-
-- Improved documentation.
-
-
-____________________________________________________________________________________
-
-
-### 0.6.2 Release Notes (2014-02-12) 
-
-
-#### New features
-
-- Additional functions for results plotting (the <code>{zoo}</code> package is required for some of them).
-
-- Add multi-objective calibration using <code>nsga2()</code> (the <code>{mco}</code> package is required).
-
-- The field Multiplier has been added in the ErrorCrit() outputs, to indicate whether the criterion is an error (to minimise) or and efficiency (to maximise).
- This allows to provide real efficiency values in the outputs e.g. NSE[Q] instead of (-1) &times; NSE[Q].
-
-
-#### Bug fixes
-
-- RC11 bug correction: the automatic selection of the warm-up period was not working properly when no data was available from warm-up (i.e. when the user had set the run to start at the very first index).
-
-- RC10 bug correction: the <code>CalibrationAlgo_HBAN()</code> function was not working in the very rare case when the diagonal search was activated and lead to a set outside the authorised range.
-
-- RC9 bug correction: the <code>CalibrationAlgo_HBAN()</code> function was not working properly with models having only one parameter.
-
-- RC8 bug correction of the <code>ModelDefaultIniOptions()</code> function (this bug was introduced in the RC7 and caused an error when <code>IndPeriod_WarmUp = NULL</code>.
-
-- RC7 bug correction of the <code>ModelDefaultIniOptions()</code> function (the automatic selection of one year for warm-up was not handling properly missing data).
-
-- RC6 correction of the help files (the description of CemaNeige parameters were inverted).
-
-- RC5 differs from previous releases in the way the data are read and stored (in a list instead of individual vectors).
- The package is similar, only the examples of Main and the files in MyScriptBlocks have changed.
- All basin data are now stored inside a list named <code>BasinData</code>. This will greatly ease the future use of Rdata files (instead of txt files) as storage format for the time series of observation. 
-
-
-#### Deprecated and defunct
-
-- <code>EfficiencyCrit()</code> have been replaced by <code>ErrorCrit()</code> to avoid misunderstanding (by default, the algorithms minimise the error criterion).
-
-
-#### Major user-visible changes
-
-- The definition of the generic function is now made in a much simpler way (e.g. see <code>DefineFunctions_Model()</code> or <code>DefineFunctions_ErrorCrit()</code>).
-
-
-#### Minor user-visible changes
-
-- Code improvements to reduce the computation time.
-
-- Clearer instructions for the adding and modification of a model.
-
-- Improvements of the documentation.
-
-
-____________________________________________________________________________________
-
-
-### 0.5.2 Release Notes (2014-02-05) 
-
-
-#### Deprecated and defunct
-
-- The <code>SelectPer</code> arguments are replaced by <code>IndPeriod</code> to ease understanding.
-
-- The <code>PE</code> arguments are replaced by <code>PotEvap()</code> to ease understanding.
-
-- The <code>Fsol</code> arguments are replaced by <code>FracSolidPrecip</code> to ease understanding.
-
-
-#### Major user-visible changes
-
-- R 2.15 in not supported by default.
-
-- The check that <code>SelectPer_Run()</code> is continuous is now made in the <code>CheckArg()</code> functions.
-
-- Check of the model functioning time step.
-
-- Name of the calibration criterion provided in <code>OutputsAlgo()</code>.
-
-
-#### Minor user-visible changes
-
-- Missing values in Fortran are now -999.999 instead of -9.999.
-
-
-____________________________________________________________________________________
-
-
-### 0.5.1 Release Notes (2014-01-27) 
-
-
-#### New features
-
-- New <code>EfficiencyCrit_NSE_sqrtQ()</code> function to compute NSE criterion on sqrt flows.
-
-
-#### Bug fixes
-
-- Incorrect arguments in the call to <code>RunModelAndCrit</code> from <code>CalibrationAlgo_optim_stats</code> and <code>CalibrationAlgo_nlminb_stats</code>.
-
-- <code>CalibrationAlgo_nlminb_stats</code> argument was wrongly defined in <code>DefineFunctions_CalibrationAlgo()</code> (<code>optim</code> instead of <code>nlminb</code>).
-
-- Format checking for <code>RunOptions</code> was incorrectly made in <code>CheckArg()</code> function.
-
-

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 <- function(InputsModel, RunOptions, InputsCrit, CalibOptions, FUN_MOD, FUN_CRIT, FUN_CALIB = Calibration_Michel, FUN_TRANSFO = NULL, verbose = TRUE) {
-  return(FUN_CALIB(InputsModel, RunOptions, InputsCrit, CalibOptions, FUN_MOD, FUN_CRIT, FUN_TRANSFO, verbose = verbose))
+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_Michel.R

-Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions,
-                               FUN_MOD, FUN_CRIT, FUN_TRANSFO = NULL, verbose = TRUE) {
-  
-  
+Calibration_Michel <- function(InputsModel,
+                               RunOptions,
+                               InputsCrit,
+                               CalibOptions,
+                               FUN_MOD,
+                               FUN_CRIT,           # deprecated
+                               FUN_TRANSFO = NULL,
+                               verbose = TRUE,
+                               ...) {
+
+
+  FUN_MOD  <- match.fun(FUN_MOD)
+
+  if (!missing(FUN_CRIT)) {
+    FUN_CRIT <- match.fun(FUN_CRIT)
+  }
+
+  # Handling 'FUN_TRANSFO' from direct argument or provided by 'CaliOptions'
+  if (!is.null(FUN_TRANSFO)) {
+    FUN_TRANSFO <- match.fun(FUN_TRANSFO)
+  } else if (!is.null(CalibOptions$FUN_TRANSFO)) {
+    FUN_TRANSFO <- CalibOptions$FUN_TRANSFO
+  } else {
+    stop("'FUN_TRANSFO' is not provided neither as 'FUN_TRANSFO' argument or in 'CaliOptions' argument")
+  }
+
   ##_____Arguments_check_____________________________________________________________________
   if (!inherits(InputsModel, "InputsModel")) {
-    stop("InputsModel must be of class 'InputsModel' \n")
-    return(NULL)
-  }  
+    stop("'InputsModel' must be of class 'InputsModel'")
+  }
   if (!inherits(RunOptions, "RunOptions")) {
-    stop("RunOptions must be of class 'RunOptions' \n")
-    return(NULL)
-  }  
+    stop("'RunOptions' must be of class 'RunOptions'")
+  }
   if (!inherits(InputsCrit, "InputsCrit")) {
-    stop("InputsCrit must be of class 'InputsCrit' \n")
-    return(NULL)
-  }  
+    stop("'InputsCrit' must be of class 'InputsCrit'")
+  }
+  if (inherits(InputsCrit, "Multi")) {
+    stop("'InputsCrit' must be of class 'Single' or 'Compo'")
+  }
+  if (inherits(InputsCrit, "Single")) {
+    listVarObs <- InputsCrit$VarObs
+  }
+  if (inherits(InputsCrit, "Compo")) {
+    listVarObs <- sapply(InputsCrit, FUN = "[[", "VarObs")
+  }
+  if ("SCA" %in% listVarObs & !"Gratio" %in% RunOptions$Outputs_Cal) {
+    warning("Missing 'Gratio' is automatically added to 'Output_Cal' in 'RunOptions' as it is necessary in the objective function for comparison with SCA")
+    RunOptions$Outputs_Cal <- c(RunOptions$Outputs_Cal, "Gratio")
+  }
+  if ("SWE" %in% listVarObs & !"SnowPack" %in% RunOptions$Outputs_Cal) {
+    warning("Missing 'SnowPack' is automatically added to 'Output_Cal' in 'RunOptions' as it is necessary in the objective function for comparison with SWE")
+    RunOptions$Outputs_Cal <- c(RunOptions$Outputs_Cal, "SnowPack")
+  }
   if (!inherits(CalibOptions, "CalibOptions")) {
-    stop("CalibOptions must be of class 'CalibOptions' \n")
-    return(NULL)
-  }  
+    stop("'CalibOptions' must be of class 'CalibOptions'")
+  }
   if (!inherits(CalibOptions, "HBAN")) {
-    stop("CalibOptions must be of class 'HBAN' if Calibration_Michel 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)
-    }
+    stop("'CalibOptions' must be of class 'HBAN' if 'Calibration_Michel' is used")
+  }
+  if (!missing(FUN_CRIT)) {
+    warning("argument 'FUN_CRIT' is deprecated. The error criterion function is now automatically get from the 'InputsCrit' object")
   }
-  
-  ##_variables_initialisation 
+
+
+  ##_variables_initialisation
   ParamFinalR <- NULL
   ParamFinalT <- NULL
   CritFinal   <- NULL
@@ -100,8 +80,7 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
     NParam <- ncol(CalibOptions$StartParamDistrib)
   }
   if (NParam > 20) {
-    stop("Calibration_Michel can handle a maximum of 20 parameters \n")
-    return(NULL)
+    stop("Calibration_Michel can handle a maximum of 20 parameters")
   }
   HistParamR    <- matrix(NA, nrow = 500 * NParam, ncol = NParam)
   HistParamT    <- matrix(NA, nrow = 500 * NParam, ncol = NParam)
@@ -112,20 +91,19 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
   CritOptim     <- +1e100
   ##_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
-  
-  
-  
+
+
+
   ##_____Parameter_Grid_Screening____________________________________________________________
-  
-  
+
+
   ##Definition_of_the_function_creating_all_possible_parameter_sets_from_different_values_for_each_parameter
+  ## use unique() to avoid duplicated values when a parameter is set
   ProposeCandidatesGrid <- function(DistribParam) {
-    NewCandidates <- expand.grid(lapply(seq_len(ncol(DistribParamR)), function(x) DistribParam[, x]))
-    NewCandidates <- unique(NewCandidates) # to avoid duplicates when a parameter is set
-    Output <- list(NewCandidates = NewCandidates)
-  }    
-  
-  
+    expand.grid(lapply(seq_len(ncol(DistribParam)), function(x) unique(DistribParam[, x])))
+  }
+
+
   ##Creation_of_new_candidates_______________________________________________
   OptimParam <- is.na(CalibOptions$FixedParam)
   if (PrefilteringType == 1) {
@@ -134,7 +112,7 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
   if (PrefilteringType == 2) {
     DistribParamR <- CalibOptions$StartParamDistrib
     DistribParamR[, !OptimParam] <- NA
-    CandidatesParamR <- ProposeCandidatesGrid(DistribParamR)$NewCandidates
+    CandidatesParamR <- ProposeCandidatesGrid(DistribParamR)
   }
   ##Remplacement_of_non_optimised_values_____________________________________
   CandidatesParamR <- apply(CandidatesParamR, 1, function(x) {
@@ -146,7 +124,7 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
   } else {
     CandidatesParamR <- cbind(CandidatesParamR)
   }
-  
+
   ##Loop_to_test_the_various_candidates______________________________________
   iNewOptim <- 0
   Ncandidates <- nrow(CandidatesParamR)
@@ -165,13 +143,14 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
         if (iNew == round(k / 10 * Ncandidates)) {
           message(" ", 10 * k, "%", appendLF = FALSE)
         }
-      } 
+      }
     }
     ##Model_run
     Param <- CandidatesParamR[iNew, ]
-    OutputsModel <- FUN_MOD(InputsModel, RunOptions, Param)
+    OutputsModel <- RunModel(InputsModel, RunOptions, Param, FUN_MOD = FUN_MOD, ...)
+
     ##Calibration_criterion_computation
-    OutputsCrit <- FUN_CRIT(InputsCrit, OutputsModel, verbose = FALSE)      
+    OutputsCrit <- ErrorCrit(InputsCrit, OutputsModel, verbose = FALSE)
     if (!is.na(OutputsCrit$CritValue)) {
       if (OutputsCrit$CritValue * OutputsCrit$Multiplier < CritOptim) {
         CritOptim <- OutputsCrit$CritValue * OutputsCrit$Multiplier
@@ -188,8 +167,8 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
   if (verbose & Ncandidates > 1) {
     message(" 100%)\n", appendLF = FALSE)
   }
-  
-  
+
+
   ##End_of_first_step_Parameter_Screening____________________________________
   ParamStartR <- CandidatesParamR[iNewOptim, ]
   if (!is.matrix(ParamStartR)) {
@@ -197,7 +176,7 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
   }
   ParamStartT <- FUN_TRANSFO(ParamStartR, "RT")
   CritStart   <- CritOptim
-  NRuns       <- NRuns+nrow(CandidatesParamR)
+  NRuns       <- NRuns + nrow(CandidatesParamR)
   if (verbose) {
     if (Ncandidates > 1) {
       message(sprintf("\t Screening completed (%s runs)", NRuns))
@@ -205,37 +184,35 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
     if (Ncandidates == 1) {
       message("\t Starting point for steepest-descent local search:")
     }
-    message("\t     Param = ", paste(sprintf("%8.3f", ParamStartR), collapse = " , "))
-    message(sprintf("\t     Crit %-12s = %.4f", CritName, CritStart * Multiplier))
+    message("\t     Param = ", paste(sprintf("%8.3f", ParamStartR), collapse = ", "))
+    message(sprintf("\t     Crit. %-12s = %.4f", CritName, CritStart * Multiplier))
   }
   ##Results_archiving________________________________________________________
   HistParamR[1, ] <- ParamStartR
   HistParamT[1, ] <- ParamStartT
   HistCrit[1, ]   <- CritStart
-  
-  
-  
-  
+
+
+
+
   ##_____Steepest_Descent_Local_Search_______________________________________________________
-  
-  
+
+
   ##Definition_of_the_function_creating_new_parameter_sets_through_a_step_by_step_progression_procedure
-  ProposeCandidatesLoc <- function(NewParamOptimT, OldParamOptimT, RangesT, OptimParam,Pace) {
+  ProposeCandidatesLoc <- function(NewParamOptimT, OldParamOptimT, RangesT, OptimParam, Pace) {
     ##Format_checking
     if (nrow(NewParamOptimT) != 1 | nrow(OldParamOptimT) != 1) {
-      stop("each input set must be a matrix of one single line \n")
-      return(NULL)
+      stop("each input set must be a matrix of one single line")
     }
     if (ncol(NewParamOptimT)!=ncol(OldParamOptimT) | ncol(NewParamOptimT) != length(OptimParam)) {
-      stop("each input set must have the same number of values \n")
-      return(NULL)
+      stop("each input set must have the same number of values")
     }
     ##Proposal_of_new_parameter_sets ###(local search providing 2 * NParam-1 new sets)
     NParam <- ncol(NewParamOptimT)
     VECT <- NULL
     for (I in 1:NParam) {
       ##We_check_that_the_current_parameter_should_indeed_be_optimised
-      if (OptimParam[I] == TRUE) {
+      if (OptimParam[I]) {
         for (J in 1:2) {
           Sign <- 2 * J - 3   #Sign can be equal to -1 or +1
           ##We_define_the_new_potential_candidate
@@ -244,10 +221,10 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
           PotentialCandidateT[1, I] <- NewParamOptimT[I] + Sign * Pace
           ##If_we_exit_the_range_of_possible_values_we_go_back_on_the_boundary
           if (PotentialCandidateT[1, I] < RangesT[1, I] ) {
-            PotentialCandidateT[1,I] <- RangesT[1, I]
+            PotentialCandidateT[1, I] <- RangesT[1, I]
           }
           if (PotentialCandidateT[1, I] > RangesT[2, I]) {
-            PotentialCandidateT[1,I] <- RangesT[2,I]
+            PotentialCandidateT[1, I] <- RangesT[2, I]
           }
           ##We_check_the_set_is_not_outside_the_range_of_possible_values
           if (NewParamOptimT[I] == RangesT[1, I] & Sign < 0) {
@@ -271,11 +248,11 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
     Output$NewCandidatesT <- matrix(VECT, ncol = NParam, byrow = TRUE)
     return(Output)
   }
-  
-  
+
+
   ##Initialisation_of_variables
   if (verbose) {
-    message("Steepest-descent local search in progress") 
+    message("Steepest-descent local search in progress")
   }
   Pace <- 0.64
   PaceDiag <- rep(0, NParam)
@@ -287,18 +264,18 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
   RangesT <- FUN_TRANSFO(RangesR, "RT")
   NewParamOptimT <- ParamStartT
   OldParamOptimT <- ParamStartT
-  
-  
+
+
   ##START_LOOP_ITER_________________________________________________________
   for (ITER in 1:(100 * NParam)) {
-    
-    
+
+
     ##Exit_loop_when_Pace_becomes_too_small___________________________________
     if (Pace < 0.01) {
       break
     }
-    
-    
+
+
     ##Creation_of_new_candidates______________________________________________
     CandidatesParamT <- ProposeCandidatesLoc(NewParamOptimT, OldParamOptimT, RangesT, OptimParam, Pace)$NewCandidatesT
     CandidatesParamR <- FUN_TRANSFO(CandidatesParamT, "TR")
@@ -312,16 +289,16 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
     } else {
       CandidatesParamR <- cbind(CandidatesParamR)
     }
-    
-    
+
+
     ##Loop_to_test_the_various_candidates_____________________________________
     iNewOptim <- 0
     for (iNew in 1:nrow(CandidatesParamR)) {
       ##Model_run
       Param <- CandidatesParamR[iNew, ]
-      OutputsModel <- FUN_MOD(InputsModel, RunOptions, Param)
+      OutputsModel <- RunModel(InputsModel, RunOptions, Param, FUN_MOD = FUN_MOD, ...)
       ##Calibration_criterion_computation
-      OutputsCrit <- FUN_CRIT(InputsCrit, OutputsModel, verbose = FALSE)      
+      OutputsCrit <- ErrorCrit(InputsCrit, OutputsModel, verbose = FALSE)
       if (!is.na(OutputsCrit$CritValue)) {
         if (OutputsCrit$CritValue * OutputsCrit$Multiplier < CritOptim) {
           CritOptim <- OutputsCrit$CritValue * OutputsCrit$Multiplier
@@ -330,8 +307,8 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
       }
     }
     NRuns <- NRuns + nrow(CandidatesParamR)
-    
-    
+
+
     ##When_a_progress_has_been_achieved_______________________________________
     if (iNewOptim != 0) {
       ##We_store_the_optimal_set
@@ -346,7 +323,7 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
       ##We_update_PaceDiag
       VectPace <- NewParamOptimT-OldParamOptimT
       for (iC in 1:NParam) {
-        if (OptimParam[iC]) { 
+        if (OptimParam[iC]) {
           PaceDiag[iC] <- CLG * PaceDiag[iC] + (1-CLG) * VectPace[iC]
         }
       }
@@ -355,8 +332,8 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
       Pace <- Pace / 2
       Compt <- 0
     }
-    
-    
+
+
     ##Test_of_an_additional_candidate_using_diagonal_progress_________________
     if (ITER > 4 * NParam) {
       NRuns <- NRuns + 1
@@ -380,9 +357,9 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
       CandidatesParamR <- FUN_TRANSFO(CandidatesParamT, "TR")
       ##Model_run
       Param <- CandidatesParamR[iNew, ]
-      OutputsModel <- FUN_MOD(InputsModel, RunOptions, Param)
+      OutputsModel <- RunModel(InputsModel, RunOptions, Param, FUN_MOD = FUN_MOD, ...)
       ##Calibration_criterion_computation
-      OutputsCrit <- FUN_CRIT(InputsCrit, OutputsModel, verbose = FALSE)
+      OutputsCrit <- ErrorCrit(InputsCrit, OutputsModel, verbose = FALSE)
       if (OutputsCrit$CritValue * OutputsCrit$Multiplier < CritOptim) {
         CritOptim <- OutputsCrit$CritValue * OutputsCrit$Multiplier
         iNewOptim <- iNew
@@ -392,37 +369,47 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
         OldParamOptimT <- NewParamOptimT
         NewParamOptimT <- matrix(CandidatesParamT[iNewOptim, 1:NParam], nrow = 1)
       }
-      
+
     }
-    
-    
+
+
     ##Results_archiving_______________________________________________________
     NewParamOptimR       <- FUN_TRANSFO(NewParamOptimT, "TR")
     HistParamR[ITER+1, ] <- NewParamOptimR
     HistParamT[ITER+1, ] <- NewParamOptimT
     HistCrit[ITER+1, ]   <- CritOptim
     ### if (verbose) { cat(paste("\t     Iter ",formatC(ITER,format="d",width=3), "    Crit ",formatC(CritOptim,format="f",digits=4), "    Pace ",formatC(Pace,format="f",digits=4), "\n",sep=""))}
-    
-    
-    
+
+
+
   } ##END_LOOP_ITER_________________________________________________________
   ITER <- ITER - 1
-  
-  
+
+
   ##Case_when_the_starting_parameter_set_remains_the_best_solution__________
-  if (CritOptim == CritStart & verbose) { 
+  if (CritOptim == CritStart & verbose) {
     message("\t No progress achieved")
   }
-  
+
   ##End_of_Steepest_Descent_Local_Search____________________________________
   ParamFinalR <- NewParamOptimR
   ParamFinalT <- NewParamOptimT
   CritFinal   <- CritOptim
   NIter       <- 1 + ITER
-  if (verbose) { 
+  if (verbose) {
     message(sprintf("\t Calibration completed (%s iterations, %s runs)", NIter, NRuns))
-    message("\t     Param = ", paste(sprintf("%8.3f", ParamFinalR), collapse = " , "))
-    message(sprintf("\t     Crit %-12s = %.4f", CritName, CritFinal * Multiplier))
+    message("\t     Param = ", paste(sprintf("%8.3f", ParamFinalR), collapse = ", "))
+    message(sprintf("\t     Crit. %-12s = %.4f", CritName, CritFinal * Multiplier))
+    if (inherits(InputsCrit, "Compo")) {
+      listweights  <- OutputsCrit$CritCompo$MultiCritWeights
+      listNameCrit <- OutputsCrit$CritCompo$MultiCritNames
+      msgForm <- paste(sprintf("%.2f", listweights), listNameCrit, sep = " * ", collapse = ", ")
+      msgForm <- unlist(strsplit(msgForm, split = ","))
+      msgFormSep <- rep(c(",", ",", ",\n\t\t    "), times = ceiling(length(msgForm)/3))[1:length(msgForm)]
+      msgForm <- paste(msgForm, msgFormSep, sep = "", collapse = "")
+      msgForm <- gsub("\\,\\\n\\\t\\\t    $|\\,$", "", msgForm)
+      message("\tFormula: sum(", msgForm, ")")
+    }
   }
   ##Results_archiving_______________________________________________________
   HistParamR <- cbind(HistParamR[1:NIter, ])
@@ -431,13 +418,13 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
   colnames(HistParamT) <- paste0("Param", 1:NParam)
   HistCrit   <- cbind(HistCrit[1:NIter, ])
   ###colnames(HistCrit) <- paste("HistCrit")
-  
+
   BoolCrit_Actual <- InputsCrit$BoolCrit
   BoolCrit_Actual[OutputsCrit$Ind_notcomputed] <- FALSE
   MatBoolCrit <- cbind(InputsCrit$BoolCrit, BoolCrit_Actual)
   colnames(MatBoolCrit) <- c("BoolCrit_Requested", "BoolCrit_Actual")
-  
-  
+
+
   ##_____Output______________________________________________________________________________
   OutputsCalib <- list(ParamFinalR = as.double(ParamFinalR), CritFinal = CritFinal * Multiplier,
                        NIter = NIter, NRuns = NRuns,
@@ -446,12 +433,7 @@ Calibration_Michel <- function(InputsModel, RunOptions, InputsCrit, CalibOptions
                        CritName = CritName, CritBestValue = CritBestValue)
   class(OutputsCalib) <- c("OutputsCalib", "HBAN")
   return(OutputsCalib)
-  
-  
-  
-}
-
-
 
 
 
+}

R/CreateCalibOptions.R

-CreateCalibOptions <-
-  function(FUN_MOD,
-           FUN_CALIB = Calibration_Michel,
-           FUN_TRANSFO = NULL,
-           FixedParam = NULL,
-           SearchRanges = NULL,
-           StartParamList = NULL,
-           StartParamDistrib = NULL) {
-    
-    ObjectClass <- NULL
-    
-    
-    ##check_FUN_MOD
-    BOOL <- FALSE
-    
-    if (identical(FUN_MOD, RunModel_GR4H)) {
-      ObjectClass <- c(ObjectClass, "GR4H")
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_GR4J)) {
-      ObjectClass <- c(ObjectClass, "GR4J")
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_GR5J)) {
-      ObjectClass <- c(ObjectClass, "GR5J")
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_GR6J)) {
-      ObjectClass <- c(ObjectClass, "GR6J")
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_GR2M)) {
-      ObjectClass <- c(ObjectClass, "GR2M")
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_GR1A)) {
-      ObjectClass <- c(ObjectClass, "GR1A")
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_CemaNeige)) {
-      ObjectClass <- c(ObjectClass, "CemaNeige")
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_CemaNeigeGR4J)) {
-      ObjectClass <- c(ObjectClass, "CemaNeigeGR4J")
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_CemaNeigeGR5J)) {
-      ObjectClass <- c(ObjectClass, "CemaNeigeGR5J")
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_CemaNeigeGR6J)) {
-      ObjectClass <- c(ObjectClass, "CemaNeigeGR6J")
-      BOOL <- TRUE
-    }
-    if (!BOOL) {
-      stop("incorrect FUN_MOD for use in CreateCalibOptions \n")
-      return(NULL)
-    }
-    
-    ##check_FUN_CALIB
-    BOOL <- FALSE
-    
-    if (identical(FUN_CALIB, Calibration_Michel)) {
-      ObjectClass <- c(ObjectClass, "HBAN")
-      BOOL <- TRUE
-    }
-    if (!BOOL) {
-      stop("incorrect FUN_CALIB for use in CreateCalibOptions \n")
-      return(NULL)
-      
-    }
-    
-    ##check_FUN_TRANSFO
-    if (is.null(FUN_TRANSFO)) {
-      ##_set_FUN1
-      if (identical(FUN_MOD, RunModel_GR4H)) {
-        FUN1 <- TransfoParam_GR4H
-      }
-      if (identical(FUN_MOD, RunModel_GR4J) |
-          identical(FUN_MOD, RunModel_CemaNeigeGR4J)) {
-        FUN1 <- TransfoParam_GR4J
-      }
-      if (identical(FUN_MOD, RunModel_GR5J) |
-          identical(FUN_MOD, RunModel_CemaNeigeGR5J)) {
-        FUN1 <- TransfoParam_GR5J
-      }
-      if (identical(FUN_MOD, RunModel_GR6J) |
-          identical(FUN_MOD, RunModel_CemaNeigeGR6J)) {
-        FUN1 <- TransfoParam_GR6J
-      }
-      if (identical(FUN_MOD, RunModel_GR2M)) {
-        FUN1 <- TransfoParam_GR2M
-      }
-      if (identical(FUN_MOD, RunModel_GR1A)) {
-        FUN1 <- TransfoParam_GR1A
-      }
-      if (identical(FUN_MOD, RunModel_CemaNeige)) {
-        FUN1 <- TransfoParam_CemaNeige
-      }
-      if (is.null(FUN1)) {
-        stop("FUN1 was not found \n")
-        return(NULL)
-      }
-      ##_set_FUN2
-      FUN2 <- TransfoParam_CemaNeige
-      
-      ##_set_FUN_TRANSFO
-      if (sum(ObjectClass %in% c("GR4H", "GR4J", "GR5J", "GR6J", "GR2M", "GR1A", "CemaNeige")) > 0) {
-        FUN_TRANSFO <- FUN1
-      } else {
-        FUN_TRANSFO <- function(ParamIn, Direction) {
-          Bool <- is.matrix(ParamIn)
-          if (Bool == FALSE) {
-            ParamIn <- rbind(ParamIn)
-          }
-          ParamOut <- NA * ParamIn
-          NParam   <- ncol(ParamIn)
-          if (NParam <= 3) {
-            ParamOut[, 1:(NParam - 2)] <- FUN1(cbind(ParamIn[, 1:(NParam - 2)]), Direction)
-          } else {
-            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 \n")
-      return(NULL)
-    }
-    
-    ##NParam
-    if ("GR4H" %in% ObjectClass) {
-      NParam <- 4
-    }
-    if ("GR4J" %in% ObjectClass) {
-      NParam <- 4
-    }
-    if ("GR5J" %in% ObjectClass) {
-      NParam <- 5
-    }
-    if ("GR6J" %in% ObjectClass) {
-      NParam <- 6
-    }
-    if ("GR2M" %in% ObjectClass) {
-      NParam <- 2
-    }
-    if ("GR1A" %in% ObjectClass) {
-      NParam <- 1
-    }
-    if ("CemaNeige" %in% ObjectClass) {
-      NParam <- 2
-    }
-    if ("CemaNeigeGR4J" %in% ObjectClass) {
-      NParam <- 6
-    }
-    if ("CemaNeigeGR5J" %in% ObjectClass) {
-      NParam <- 7
-    }
-    if ("CemaNeigeGR6J" %in% ObjectClass) {
-      NParam <- 8
-    }
-    
-    ##check_FixedParam
-    if (is.null(FixedParam)) {
-      FixedParam <- rep(NA, NParam)
-    } else {
-      if (!is.vector(FixedParam)) {
-        stop("FixedParam must be a vector \n")
-        return(NULL)
-      }
-      if (length(FixedParam) != NParam) {
-        stop("Incompatibility between FixedParam length and FUN_MOD \n")
-        return(NULL)
-      }
-      if (all(!is.na(FixedParam))) {
-        stop("At least one parameter must be not set (NA) \n")
-        return(NULL)
-      }
-      if (all(is.na(FixedParam))) {
-        warning("You have not set any parameter in \"FixedParam\" \n")
-      }
-    }
-    
-    ##check_SearchRanges
-    if (is.null(SearchRanges)) {
-      ParamT <-  matrix(c(rep(-9.99, NParam), rep(+9.99, NParam)),
-                        ncol = NParam, byrow = TRUE)
-      
-      SearchRanges <- TransfoParam(ParamIn = ParamT, Direction = "TR", FUN_TRANSFO = FUN_TRANSFO)
-      
-    } else {
-      if (!is.matrix(SearchRanges)) {
-        stop("SearchRanges must be a matrix \n")
-        return(NULL)
-      }
-      if (!is.numeric(SearchRanges)) {
-        stop("SearchRanges must be a matrix of numeric values \n")
-        return(NULL)
-      }
-      if (sum(is.na(SearchRanges)) != 0) {
-        stop("SearchRanges must not include NA values \n")
-        return(NULL)
-      }
-      if (nrow(SearchRanges) != 2) {
-        stop("SearchRanges must have 2 rows \n")
-        return(NULL)
-      }
-      if (ncol(SearchRanges) != NParam) {
-        stop("Incompatibility between SearchRanges ncol and FUN_MOD \n")
-        return(NULL)
-      }
-    }
-    
-    ##check_StartParamList_and_StartParamDistrib__default_values
-    if (("HBAN"  %in% ObjectClass & is.null(StartParamList) & is.null(StartParamDistrib))) {
-      if ("GR4H" %in% ObjectClass) {
-        ParamT <- matrix(c(+5.12, -1.18, +4.34, -9.69,
-                           +5.58, -0.85, +4.74, -9.47,
-                           +6.01, -0.50, +5.14, -8.87), ncol = NParam,  byrow = TRUE)
-      }
-      if ("GR4J" %in% ObjectClass) {
-        ParamT <- matrix(c(+5.13, -1.60, +3.03, -9.05,
-                           +5.51, -0.61, +3.74, -8.51,
-                           +6.07, -0.02, +4.42, -8.06),  ncol = NParam, byrow = TRUE)
-      }
-      if ("GR5J" %in% ObjectClass) {
-        ParamT <- matrix(c(+5.17, -1.13, +3.08, -9.37, -7.45,
-                           +5.55, -0.46, +3.75, -9.09, -4.69,
-                           +6.10, -0.11, +4.43, -8.60, -0.66), ncol = NParam, byrow = TRUE)
-        
-      }
-      if ("GR6J" %in% ObjectClass) {
-        ParamT <- matrix(c(+3.60, -1.00, +3.30, -9.10, -0.90, +3.00,
-                           +3.90, -0.50, +4.10, -8.70, +0.10, +4.00,
-                           +4.50, +0.50, +5.00, -8.10, +1.10, +5.00), ncol = NParam, byrow = TRUE)
-      }
-      if ("GR2M" %in% ObjectClass) {
-        ParamT <- matrix(c(+5.03, -7.15,
-                           +5.22, -6.74,
-                           +5.85, -6.37), ncol = NParam, byrow = TRUE)
-      }
-      if ("GR1A" %in% ObjectClass) {
-        ParamT <- matrix(c(-1.69,
-                           -0.38,
-                           +1.39), ncol = NParam, byrow = TRUE)
-      }
-      if ("CemaNeige" %in% ObjectClass) {
-        ParamT <- matrix(c(-9.96, +6.63,
-                           -9.14, +6.90,
-                           +4.10, +7.21), ncol = NParam, byrow = TRUE)
-      }
-      if ("CemaNeigeGR4J" %in% ObjectClass) {
-        ParamT <- matrix(c(+5.13, -1.60, +3.03, -9.05, -9.96, +6.63,
-                           +5.51, -0.61, +3.74, -8.51, -9.14, +6.90,
-                           +6.07, -0.02, +4.42, -8.06, +4.10, +7.21), ncol = NParam, byrow = TRUE)
-      }
-      if ("CemaNeigeGR5J" %in% ObjectClass) {
-        ParamT <- matrix(c(+5.17, -1.13, +3.08, -9.37, -7.45, -9.96, +6.63,
-                           +5.55, -0.46, +3.75, -9.09, -4.69, -9.14, +6.90,
-                           +6.10, -0.11, +4.43, -8.60, -0.66, +4.10, +7.21), ncol = NParam, byrow = TRUE)
-      }
-      if ("CemaNeigeGR6J" %in% ObjectClass) {
-        ParamT <- matrix(c(+3.60, -1.00, +3.30, -9.10, -0.90, +3.00, -9.96, +6.63,
-                           +3.90, -0.50, +4.10, -8.70, +0.10, +4.00, -9.14, +6.90,
-                           +4.50, +0.50, +5.00, -8.10, +1.10, +5.00, +4.10, +7.21), ncol = NParam, byrow = TRUE)
-      }
-      
-      StartParamList    <- NULL
-      StartParamDistrib <- TransfoParam(ParamIn = ParamT, Direction = "TR", FUN_TRANSFO = FUN_TRANSFO)
-      
-    }
-    
-    ##check_StartParamList_and_StartParamDistrib__format
-    if ("HBAN" %in% ObjectClass & !is.null(StartParamList)) {
-      if (!is.matrix(StartParamList)) {
-        stop("StartParamList must be a matrix \n")
-        return(NULL)
-      }
-      if (!is.numeric(StartParamList)) {
-        stop("StartParamList must be a matrix of numeric values \n")
-        return(NULL)
-      }
-      if (sum(is.na(StartParamList)) != 0) {
-        stop("StartParamList must not include NA values \n")
-        return(NULL)
-      }
-      if (ncol(StartParamList) != NParam) {
-        stop("Incompatibility between StartParamList ncol and FUN_MOD \n")
-        return(NULL)
-      }
-    }
-    if ("HBAN" %in% ObjectClass & !is.null(StartParamDistrib)) {
-      if (!is.matrix(StartParamDistrib)) {
-        stop("StartParamDistrib must be a matrix \n")
-        return(NULL)
-      }
-      if (!is.numeric(StartParamDistrib[1, ])) {
-        stop("StartParamDistrib must be a matrix of numeric values \n")
-        return(NULL)
-      }
-      if (sum(is.na(StartParamDistrib[1, ])) != 0) {
-        stop("StartParamDistrib must not include NA values on the first line \n")
-        return(NULL)
-      }
-      if (ncol(StartParamDistrib) != NParam) {
-        stop("Incompatibility between StartParamDistrib ncol and FUN_MOD \n")
-        return(NULL)
-      }
-    }
-    
-    
-    ##Create_CalibOptions
-    CalibOptions <- list(FixedParam = FixedParam, SearchRanges = SearchRanges)
-    
-    if (!is.null(StartParamList)) {
-      CalibOptions <- c(CalibOptions, list(StartParamList = StartParamList))
-    }
-    if (!is.null(StartParamDistrib)) {
-      CalibOptions <- c(CalibOptions, list(StartParamDistrib = StartParamDistrib))
-    }
-    class(CalibOptions) <- c("CalibOptions", ObjectClass)
-    
-    return(CalibOptions)
-    
+CreateCalibOptions <- function(FUN_MOD,
+                               FUN_CALIB = Calibration_Michel,
+                               FUN_TRANSFO = NULL,
+                               IsHyst = FALSE,
+                               IsSD = FALSE,
+                               FixedParam = NULL,
+                               SearchRanges = NULL,
+                               StartParamList = NULL,
+                               StartParamDistrib = NULL) {
+
+  ObjectClass <- NULL
+
+  FUN_MOD     <- match.fun(FUN_MOD)
+  FUN_CALIB   <- match.fun(FUN_CALIB)
+  if (!is.null(FUN_TRANSFO)) {
+    FUN_TRANSFO <- match.fun(FUN_TRANSFO)
   }
+  if (!is.logical(IsHyst) | length(IsHyst) != 1L) {
+    stop("'IsHyst' must be a logical of length 1")
+  }
+  if (!is.logical(IsSD) | length(IsSD) != 1L) {
+    stop("'IsSD' must be a logical of length 1")
+  }
+
+  ## check FUN_MOD
+  FeatFUN_MOD <- .GetFeatModel(FUN_MOD = FUN_MOD)
+  FeatFUN_MOD$IsHyst <- IsHyst
+  FeatFUN_MOD$IsSD <- IsSD
+  ObjectClass <- FeatFUN_MOD$Class
+
+  if (identical(FUN_MOD, RunModel_Lag) && IsSD) {
+      stop("RunModel_Lag should not be used with 'IsSD=TRUE'")
+  }
+  if (IsHyst) {
+    ObjectClass <- c(ObjectClass, "hysteresis")
+  }
+  if (IsSD) {
+    ObjectClass <- c(ObjectClass, "SD")
+  }
+
+  ## check FUN_CALIB
+  BOOL <- FALSE
+
+  if (identical(FUN_CALIB, Calibration_Michel)) {
+    ObjectClass <- c(ObjectClass, "HBAN")
+    BOOL <- TRUE
+  }
+  if (!BOOL) {
+    stop("incorrect 'FUN_CALIB' for use in 'CreateCalibOptions'")
+    return(NULL)
+
+  }
+
+  ## check FUN_TRANSFO
+  if (is.null(FUN_TRANSFO)) {
+    FUN_TRANSFO <- .FunTransfo(FeatFUN_MOD)
+  }
+
+  ## NParam
+  NParam <- FeatFUN_MOD$NbParam
+
+  if (IsHyst) {
+    NParam <- NParam + 2
+  }
+  if (IsSD) {
+    NParam <- NParam + 1
+  }
+
+  ## check FixedParam
+  if (is.null(FixedParam)) {
+    FixedParam <- rep(NA, NParam)
+  } else {
+    if (!is.vector(FixedParam)) {
+      stop("FixedParam must be a vector")
+    }
+    if (length(FixedParam) != NParam) {
+      stop("Incompatibility between 'FixedParam' length and 'FUN_MOD'")
+    }
+    if (all(!is.na(FixedParam))) {
+      stop("At least one parameter must be not set (NA)")
+    }
+    if (all(is.na(FixedParam))) {
+      warning("You have not set any parameter in 'FixedParam'")
+    }
+  }
+
+  ## check SearchRanges
+  if (is.null(SearchRanges)) {
+    ParamT <- matrix(c(rep(-9.99, NParam), rep(+9.99, NParam)),
+                     ncol = NParam, byrow = TRUE)
+    SearchRanges <- TransfoParam(ParamIn = ParamT, Direction = "TR", FUN_TRANSFO = FUN_TRANSFO)
+
+  } else {
+    if (!is.matrix(SearchRanges)) {
+      stop("'SearchRanges' must be a matrix")
+    }
+    if (!is.numeric(SearchRanges)) {
+      stop("'SearchRanges' must be a matrix of numeric values")
+    }
+    if (sum(is.na(SearchRanges)) != 0) {
+      stop("'SearchRanges' must not include NA values")
+    }
+    if (nrow(SearchRanges) != 2) {
+      stop("'SearchRanges' must have 2 rows")
+    }
+    if (ncol(SearchRanges) != NParam) {
+      stop("Incompatibility between 'SearchRanges' ncol and 'FUN_MOD'")
+    }
+  }
+
+  ## check StartParamList and StartParamDistrib default values
+  if (("HBAN"  %in% ObjectClass & is.null(StartParamList) & is.null(StartParamDistrib))) {
+    if ("GR4H" == FeatFUN_MOD$CodeMod) {
+      ParamT <- matrix(c(+5.12, -1.18, +4.34, -9.69,
+                         +5.58, -0.85, +4.74, -9.47,
+                         +6.01, -0.50, +5.14, -8.87), ncol = 4, byrow = TRUE)
+    }
+    if (("GR5H" == FeatFUN_MOD$CodeMod) & ("interception" %in% ObjectClass)) {
+      ParamT <- matrix(c(+3.46, -1.25, +4.04, -9.53, -9.34,
+                         +3.74, -0.41, +4.78, -8.94, -3.33,
+                         +4.29, +0.16, +5.39, -7.39, +3.33), ncol = 5, byrow = TRUE)
+    }
+    if (("GR5H" == FeatFUN_MOD$CodeMod) & !("interception" %in% ObjectClass)) {
+      ParamT <- matrix(c(+3.28, -0.39, +4.14, -9.54, -7.49,
+                         +3.62, -0.19, +4.80, -9.00, -6.31,
+                         +4.01, -0.04, +5.43, -7.53, -5.33), ncol = 5, byrow = TRUE)
+    }
+    if ("GR4J" == FeatFUN_MOD$CodeMod) {
+      ParamT <- matrix(c(+5.13, -1.60, +3.03, -9.05,
+                         +5.51, -0.61, +3.74, -8.51,
+                         +6.07, -0.02, +4.42, -8.06), ncol = 4, byrow = TRUE)
+    }
+    if ("GR5J" == FeatFUN_MOD$CodeMod) {
+      ParamT <- matrix(c(+5.17, -1.13, +3.08, -9.37, -7.45,
+                         +5.55, -0.46, +3.75, -9.09, -4.69,
+                         +6.10, -0.11, +4.43, -8.60, -0.66), ncol = 5, byrow = TRUE)
+
+    }
+    if ("GR6J" == FeatFUN_MOD$CodeMod) {
+      ParamT <- matrix(c(+3.60, -1.00, +3.30, -9.10, -0.90, +3.00,
+                         +3.90, -0.50, +4.10, -8.70, +0.10, +4.00,
+                         +4.50, +0.50, +5.00, -8.10, +1.10, +5.00), ncol = 6, byrow = TRUE)
+    }
+    if ("GR2M" == FeatFUN_MOD$CodeMod) {
+      ParamT <- matrix(c(+5.03, -7.15,
+                         +5.22, -6.74,
+                         +5.85, -6.37), ncol = 2, byrow = TRUE)
+    }
+    if ("GR1A" == FeatFUN_MOD$CodeMod) {
+      ParamT <- matrix(c(-1.69,
+                         -0.38,
+                         +1.39), ncol = 1, byrow = TRUE)
+    }
+
+
+    if ("CemaNeige" == FeatFUN_MOD$CodeMod) {
+      ParamT <- matrix(c(-9.96, +6.63,
+                         -9.14, +6.90,
+                         +4.10, +7.21), ncol = 2, byrow = TRUE)
+    }
+    if ("CemaNeigeGR4H" == FeatFUN_MOD$CodeMod) {
+      ParamT <- matrix(c(+5.12, -1.18, +4.34, -9.69, -9.96, +6.63,
+                         +5.58, -0.85, +4.74, -9.47, -9.14, +6.90,
+                         +6.01, -0.50, +5.14, -8.87, +4.10, +7.21), ncol = 6, byrow = TRUE)
+    }
+    if (("CemaNeigeGR5H" == FeatFUN_MOD$CodeMod) & ("interception" %in% ObjectClass)) {
+      ParamT <- matrix(c(+3.46, -1.25, +4.04, -9.53, -9.34, -9.96, +6.63,
+                         +3.74, -0.41, +4.78, -8.94, -3.33, -9.14, +6.90,
+                         +4.29, +0.16, +5.39, -7.39, +3.33, +4.10, +7.21), ncol = 7, byrow = TRUE)
+    }
+    if (("CemaNeigeGR5H" == FeatFUN_MOD$CodeMod) & !("interception" %in% ObjectClass)) {
+      ParamT <- matrix(c(+3.28, -0.39, +4.14, -9.54, -7.49, -9.96, +6.63,
+                         +3.62, -0.19, +4.80, -9.00, -6.31, -9.14, +6.90,
+                         +4.01, -0.04, +5.43, -7.53, -5.33, +4.10, +7.21), ncol = 7, byrow = TRUE)
+    }
+    if ("CemaNeigeGR4J" == FeatFUN_MOD$CodeMod) {
+      ParamT <- matrix(c(+5.13, -1.60, +3.03, -9.05, -9.96, +6.63,
+                         +5.51, -0.61, +3.74, -8.51, -9.14, +6.90,
+                         +6.07, -0.02, +4.42, -8.06, +4.10, +7.21), ncol = 6, byrow = TRUE)
+    }
+    if ("CemaNeigeGR5J" == FeatFUN_MOD$CodeMod) {
+      ParamT <- matrix(c(+5.17, -1.13, +3.08, -9.37, -7.45, -9.96, +6.63,
+                         +5.55, -0.46, +3.75, -9.09, -4.69, -9.14, +6.90,
+                         +6.10, -0.11, +4.43, -8.60, -0.66, +4.10, +7.21), ncol = 7, byrow = TRUE)
+    }
+    if ("CemaNeigeGR6J" == FeatFUN_MOD$CodeMod) {
+      ParamT <- matrix(c(+3.60, -1.00, +3.30, -9.10, -0.90, +3.00, -9.96, +6.63,
+                         +3.90, -0.50, +4.10, -8.70, +0.10, +4.00, -9.14, +6.90,
+                         +4.50, +0.50, +5.00, -8.10, +1.10, +5.00, +4.10, +7.21), ncol = 8, byrow = TRUE)
+    }
+
+    if (IsHyst) {
+      ParamTHyst <- matrix(c(-7.00, -7.00,
+                             -0.00, -0.00,
+                             +7.00, +7.00), ncol = 2, byrow = TRUE)
+      ParamT <- cbind(ParamT, ParamTHyst)
+    }
+    if (IsSD) {
+      ParamTSD <- matrix(c(-8.75,
+                           -7.50,
+                           -5.00), ncol = 1, byrow = TRUE)
+      ParamT <- cbind(ParamTSD, ParamT)
+    }
+
+    StartParamList    <- NULL
+    StartParamDistrib <- TransfoParam(ParamIn = ParamT, Direction = "TR", FUN_TRANSFO = FUN_TRANSFO)
+
+  }
+
+  ## check StartParamList and StartParamDistrib format
+  if ("HBAN" %in% ObjectClass & !is.null(StartParamList)) {
+    if (!is.matrix(StartParamList)) {
+      stop("'StartParamList' must be a matrix")
+    }
+    if (!is.numeric(StartParamList)) {
+      stop("'StartParamList' must be a matrix of numeric values")
+    }
+    if (sum(is.na(StartParamList)) != 0) {
+      stop("'StartParamList' must not include NA values")
+    }
+    if (ncol(StartParamList) != NParam) {
+      stop("Incompatibility between 'StartParamList' ncol and 'FUN_MOD'")
+    }
+  }
+  if ("HBAN" %in% ObjectClass & !is.null(StartParamDistrib)) {
+    if (!is.matrix(StartParamDistrib)) {
+      stop("'StartParamDistrib' must be a matrix")
+    }
+    if (!is.numeric(StartParamDistrib[1, ])) {
+      stop("'StartParamDistrib' must be a matrix of numeric values")
+    }
+    if (sum(is.na(StartParamDistrib[1, ])) != 0) {
+      stop("'StartParamDistrib' must not include NA values on the first line")
+    }
+    if (ncol(StartParamDistrib) != NParam) {
+      stop("Incompatibility between 'StartParamDistrib' ncol and 'FUN_MOD'")
+    }
+  }
+
+
+  ##Create_CalibOptions
+  CalibOptions <- list(FixedParam = FixedParam, SearchRanges = SearchRanges, FUN_TRANSFO = FUN_TRANSFO)
+
+  if (!is.null(StartParamList)) {
+    CalibOptions <- c(CalibOptions, list(StartParamList = StartParamList))
+  }
+  if (!is.null(StartParamDistrib)) {
+    CalibOptions <- c(CalibOptions, list(StartParamDistrib = StartParamDistrib))
+  }
+  class(CalibOptions) <- c("CalibOptions", ObjectClass)
+
+  return(CalibOptions)
+
+}

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,
-                            ProdStore = 350, RoutStore = 90, ExpStore = NULL,
+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
-  
-  
-  ## check FUN_MOD
-  BOOL <- FALSE
-  if (identical(FUN_MOD, RunModel_GR4H)) {
-    ObjectClass <- c(ObjectClass, "GR", "hourly")
-    BOOL <- TRUE
-  }
-  if (identical(FUN_MOD, RunModel_GR4J) |
-      identical(FUN_MOD, RunModel_GR5J) |
-      identical(FUN_MOD, RunModel_GR6J)) {
-    ObjectClass <- c(ObjectClass, "GR", "daily")
-    BOOL <- TRUE
-  }
-  if (identical(FUN_MOD, RunModel_GR2M)) {
-    ObjectClass <- c(ObjectClass, "GR", "monthly")
-    BOOL <- TRUE
-  }
-  if (identical(FUN_MOD, RunModel_GR1A)) {
-    stop("'RunModel_GR1A' does not require 'IniStates' object")
-  }
-  if (identical(FUN_MOD, RunModel_CemaNeige)) {
-    ObjectClass <- c(ObjectClass, "CemaNeige", "daily")
-    BOOL <- TRUE
-  }
-  if (identical(FUN_MOD, RunModel_CemaNeigeGR4J) |
-      identical(FUN_MOD, RunModel_CemaNeigeGR5J) |
-      identical(FUN_MOD, RunModel_CemaNeigeGR6J)) {
-    ObjectClass <- c(ObjectClass, "GR", "CemaNeige", "daily")
-    BOOL <- TRUE
+
+  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 (!BOOL) {
-    stop("Incorrect 'FUN_MOD' for use in 'CreateIniStates'")
-    return(NULL)
+  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'")
-    return(NULL)
   }
   if ("GR" %in% ObjectClass & !inherits(InputsModel, "GR")) {
     stop("'InputsModel' must be of class 'GR'")
-    return(NULL)
   }
   if ("CemaNeige" %in% ObjectClass &
       !inherits(InputsModel, "CemaNeige")) {
     stop("'InputsModel' must be of class 'CemaNeige'")
-    return(NULL)
   }
-  
-  
+
+
   ## 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")
-      return(NULL)
     }
   } else if (!is.null(ExpStore)) {
     if (verbose) {
-      warning(sprintf("'%s' does not require 'ExpStore'. Value set to NA", as.character(substitute(FUN_MOD))))
+      warning(sprintf("'%s' does not require 'ExpStore'. Value set to NA", FeatFUN_MOD$NameFunMod))
     }
     ExpStore <- Inf
   }
-  
+
   if (identical(FUN_MOD, RunModel_GR2M)) {
     if (!is.null(UH1)) {
       if (verbose) {
-        warning(sprintf("'%s' does not require 'UH1'. Values set to NA", as.character(substitute(FUN_MOD))))
+        warning(sprintf("'%s' does not require 'UH1'. Values set to NA", FeatFUN_MOD$NameFunMod))
       }
       UH1 <- rep(Inf, UH1n)
     }
     if (!is.null(UH2)) {
       if (verbose) {
-        warning(sprintf("'%s' does not require 'UH2'. Values set to NA", as.character(substitute(FUN_MOD))))
+        warning(sprintf("'%s' does not require 'UH2'. Values set to NA", FeatFUN_MOD$NameFunMod))
       }
       UH2 <- rep(Inf, UH2n)
     }
   }
-  
+
   if ((identical(FUN_MOD, RunModel_GR5J) | identical(FUN_MOD, RunModel_CemaNeigeGR5J)) & !is.null(UH1)) {
     if (verbose) {
-      warning(sprintf("'%s' does not require 'UH1'. Values set to NA", as.character(substitute(FUN_MOD))))
+      warning(sprintf("'%s' does not require 'UH1'. Values set to NA", FeatFUN_MOD$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$NameFunMod))
+    }
+    IntStore <- Inf
+  }
+
   if ("CemaNeige" %in% ObjectClass & ! "GR" %in% ObjectClass) {
     if (!is.null(ProdStore)) {
       if (verbose) {
-        warning(sprintf("'%s' does not require 'ProdStore'. Values set to NA", as.character(substitute(FUN_MOD))))
+        warning(sprintf("'%s' does not require 'ProdStore'. Values set to NA", FeatFUN_MOD$NameFunMod))
       }
     }
     ProdStore <- Inf
     if (!is.null(RoutStore)) {
       if (verbose) {
-        warning(sprintf("'%s' does not require 'RoutStore'. Values set to NA", as.character(substitute(FUN_MOD))))
+        warning(sprintf("'%s' does not require 'RoutStore'. Values set to NA", FeatFUN_MOD$NameFunMod))
       }
     }
     RoutStore <- Inf
     if (!is.null(ExpStore)) {
       if (verbose) {
-        warning(sprintf("'%s' does not require 'ExpStore'. Values set to NA", as.character(substitute(FUN_MOD))))
+        warning(sprintf("'%s' does not require 'ExpStore'. Values set to NA", FeatFUN_MOD$NameFunMod))
       }
     }
     ExpStore <- Inf
+    if (!is.null(IntStore)) {
+      if (verbose) {
+        warning(sprintf("'%s' does not require 'IntStore'. Values set to NA", FeatFUN_MOD$NameFunMod))
+      }
+    }
+    IntStore <- Inf
     if (!is.null(UH1)) {
       if (verbose) {
-        warning(sprintf("'%s' does not require 'UH1'. Values set to NA", as.character(substitute(FUN_MOD))))
+        warning(sprintf("'%s' does not require 'UH1'. Values set to NA", FeatFUN_MOD$NameFunMod))
       }
     }
     UH1 <- rep(Inf, UH1n)
     if (!is.null(UH2)) {
       if (verbose) {
-        warning(sprintf("'%s' does not require 'UH2'. Values set to NA", as.character(substitute(FUN_MOD))))
+        warning(sprintf("'%s' does not require 'UH2'. Values set to NA", FeatFUN_MOD$NameFunMod))
       }
     }
     UH2 <- rep(Inf, UH2n)
   }
-  if("CemaNeige" %in% ObjectClass &
+  if (IsIntStore & is.null(IntStore)) {
+      stop(sprintf("'%s' need values for 'IntStore'", FeatFUN_MOD$NameFunMod))
+  }
+  if ("CemaNeige" %in% ObjectClass & !IsHyst &
      (is.null(GCemaNeigeLayers) | is.null(eTGCemaNeigeLayers))) {
-    stop("'RunModel_CemaNeigeGR*' need values for 'GCemaNeigeLayers' and 'GCemaNeigeLayers'")
-    return(NULL)
+      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$NameFunMod))
+    }
+    GthrCemaNeigeLayers    <- Inf
+    GlocmaxCemaNeigeLayers <- Inf
   }
-  if(!"CemaNeige" %in% ObjectClass &
-     (!is.null(GCemaNeigeLayers) | !is.null(eTGCemaNeigeLayers))) {
+  if (!"CemaNeige" %in% ObjectClass &
+     (!is.null(GCemaNeigeLayers) | !is.null(eTGCemaNeigeLayers) | !is.null(GthrCemaNeigeLayers) | !is.null(GlocmaxCemaNeigeLayers))) {
     if (verbose) {
-      warning(sprintf("'%s' does not require 'GCemaNeigeLayers' and 'GCemaNeigeLayers'. Values set to NA", as.character(substitute(FUN_MOD))))
+      warning(sprintf("'%s' does not require 'GCemaNeigeLayers' 'GCemaNeigeLayers', 'GthrCemaNeigeLayers' and 'GlocmaxCemaNeigeLayers'. Values set to NA", FeatFUN_MOD$NameFunMod))
     }
-    GCemaNeigeLayers   <- Inf
-    eTGCemaNeigeLayers <- Inf
+    GCemaNeigeLayers       <- Inf
+    eTGCemaNeigeLayers     <- Inf
+    GthrCemaNeigeLayers    <- Inf
+    GlocmaxCemaNeigeLayers <- Inf
   }
-  
-  
+
+
   ## set states
-  if("CemaNeige" %in% ObjectClass) {
+  if ("CemaNeige" %in% ObjectClass) {
     NLayers <- length(InputsModel$LayerPrecip)
   } else {
     NLayers <- 1
   }
-  
-  
+
+
   ## manage NULL values
   if (is.null(ExpStore)) {
-    ExpStore <- Inf 
+    ExpStore <- Inf
+  }
+  if (is.null(IntStore)) {
+    IntStore <- Inf
   }
   if (is.null(UH1)) {
     if ("hourly"  %in% ObjectClass) {
@@ -165,7 +172,7 @@ CreateIniStates <- function(FUN_MOD, InputsModel,
     } else {
       k <- 1
     }
-    UH1 <- rep(Inf, 20 * k)
+    UH1 <- rep(Inf, UH1n * k)
   }
   if (is.null(UH2)) {
     if ("hourly"  %in% ObjectClass) {
@@ -173,7 +180,7 @@ CreateIniStates <- function(FUN_MOD, InputsModel,
     } else {
       k <- 1
     }
-    UH2 <- rep(Inf, 40 * k)
+    UH2 <- rep(Inf, UH2n * k)
   }
   if (is.null(GCemaNeigeLayers)) {
     GCemaNeigeLayers <- rep(Inf, NLayers)
@@ -181,19 +188,29 @@ CreateIniStates <- function(FUN_MOD, InputsModel,
   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) |
+  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', 'UH1', 'UH2', 'GCemaNeigeLayers'")
+    stop("Negative values are not allowed for any of 'ProdStore', 'RoutStore', 'IntStore', 'UH1', 'UH2', 'GCemaNeigeLayers'")
   }
-  
-  
+
+
   ## check length
   if (!is.numeric(ProdStore) || length(ProdStore) != 1L) {
-    print(ProdStore)
     stop("'ProdStore' must be numeric of length one")
   }
   if (!is.numeric(RoutStore) || length(RoutStore) != 1L) {
@@ -202,16 +219,19 @@ CreateIniStates <- function(FUN_MOD, InputsModel,
   if (!is.numeric(ExpStore) || length(ExpStore) != 1L) {
     stop("'ExpStore' must be numeric of length one")
   }
-  if ( "hourly" %in% ObjectClass & (!is.numeric(UH1) || length(UH1) != 480L)) {
+  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) != 20L)) {
+  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) != 960L)) {
+  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) != 40L)) {
+  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) {
@@ -220,18 +240,54 @@ CreateIniStates <- function(FUN_MOD, InputsModel,
   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),
+  IniStates <- list(Store = list(Prod = ProdStore, Rout = RoutStore, Exp = ExpStore, Int = IntStore),
                     UH = list(UH1 = UH1, UH2 = UH2),
-                    CemaNeigeLayers = list(G = GCemaNeigeLayers, eTG = eTGCemaNeigeLayers))
+                    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

 CreateInputsCrit <- function(FUN_CRIT,
                              InputsModel,
                              RunOptions,
-                             Qobs,
+                             Obs,
+                             VarObs = "Q",
                              BoolCrit = NULL,
                              transfo = "",
-                             Ind_zeroes = NULL,
+                             Weights = NULL,
                              epsilon = NULL,
-                             verbose = TRUE) {
-  
-  
+                             warnings = TRUE) {
+
+
   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' or 'sort' \n")
-      return(NULL)
-    }
-    if (!is.vector(transfo)) {
-      stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' or 'sort' \n")
-      return(NULL)
-    }
-    if (length(transfo) != 1) {
-      stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' or 'sort' \n")
-      return(NULL)
-    }
-    if (!is.character(transfo)) {
-      stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' or 'sort' \n")
-      return(NULL)
-    }
-    if (! transfo %in% c("", "sqrt", "log", "inv", "sort")) {
-      stop("transfo must be a chosen among the following: '', 'sqrt', 'log' or 'inv' or 'sort' \n")
-      return(NULL)
-    }
-    
-    if (!missing(Ind_zeroes)) {
-      warning("Deprecated \"Ind_zeroes\" argument")
-    }
-
-    if (!is.null(epsilon)) {
-      if (!is.vector(epsilon) | length(epsilon) != 1 | !is.numeric(epsilon) | any(epsilon <= 0)) {
-        stop("epsilon must a be single positive value \n")
-        return(NULL)
-      }
-    } else if (transfo %in% c("log", "inv") & any(Qobs %in% 0) & verbose) {
-      warning("zeroes detected in Qobs: the corresponding time-steps will be exclude by the 'ErrorCrit*' functions if the epsilon agrument = NULL")
-    }
-    
-    if (transfo == "log" & verbose) {
-      warn_log_kge <- "we do not advise using the %s with a log transformation on Qobs (see the details part in the 'CreateInputsCrit' help)"
-      if (identical(FUN_CRIT, ErrorCrit_KGE)) {
-          warning(sprintf(warn_log_kge, "KGE"))
+
+
+  ## ---------- 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))
         }
-      if (identical(FUN_CRIT, ErrorCrit_KGE2)) {
-          warning(sprintf(warn_log_kge, "KGE'"))
-      }
-    }
-    
-    ##Create_InputsCrit
-    InputsCrit <- list(BoolCrit   = BoolCrit,
-                       Qobs       = Qobs,
-                       transfo    = transfo,
-                       epsilon    = epsilon)
-    
-    class(InputsCrit) <- c("InputsCrit", ObjectClass)
-    
-    return(InputsCrit)
-    
-    
-    
+      }
+    }
   }
+
+  ## 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))
+}

R/CreateInputsModel.R

@@ -4,321 +4,296 @@ CreateInputsModel <- function(FUN_MOD,
                               PotEvap = NULL,
                               TempMean = NULL, TempMin = NULL, TempMax = NULL,
                               ZInputs = NULL, HypsoData = NULL, NLayers = 5,
+                              Qupstream = NULL, LengthHydro = NULL, BasinAreas = NULL,
+                              QupstrUnit = "mm",
                               verbose = TRUE) {
-    
-    
-    ObjectClass <- NULL
-    
-    ##check_FUN_MOD
-    BOOL <- FALSE
-    if (identical(FUN_MOD, RunModel_GR4H)) {
-      ObjectClass <- c(ObjectClass, "hourly", "GR")
-      
-      TimeStep <- as.integer(60 * 60)
-      
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_GR4J) |
-        identical(FUN_MOD, RunModel_GR5J) |
-        identical(FUN_MOD, RunModel_GR6J)) {
-      ObjectClass <- c(ObjectClass, "daily", "GR")
-      
-      TimeStep <- as.integer(24 * 60 * 60)
-      
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_GR2M)) {
-      ObjectClass <- c(ObjectClass, "GR", "monthly")
-      
-      TimeStep <- as.integer(c(28, 29, 30, 31) * 24 * 60 * 60)
-      
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_GR1A)) {
-      ObjectClass <- c(ObjectClass, "GR", "yearly")
-      
-      TimeStep <- as.integer(c(365, 366) * 24 * 60 * 60)
-      
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_CemaNeige)) {
-      ObjectClass <- c(ObjectClass, "daily", "CemaNeige")
-      
-      TimeStep <- as.integer(24 * 60 * 60)
-      
-      BOOL <- TRUE
-    }
-    if (identical(FUN_MOD, RunModel_CemaNeigeGR4J) |
-        identical(FUN_MOD, RunModel_CemaNeigeGR5J) |
-        identical(FUN_MOD, RunModel_CemaNeigeGR6J)) {
-      ObjectClass <- c(ObjectClass, "daily", "GR", "CemaNeige")
-      
-      TimeStep <- as.integer(24 * 60 * 60)
-      
-      BOOL <- TRUE
-    }
-    if (!BOOL) {
-      stop("Incorrect FUN_MOD for use in CreateInputsModel \n")
-      return(NULL)
-    }
-    
-    ##check_arguments
-    if ("GR" %in% ObjectClass | "CemaNeige" %in% ObjectClass) {
-      if (is.null(DatesR)) {
-        stop("DatesR is missing \n")
-        return(NULL)
-      }
-      if ("POSIXlt" %in% class(DatesR) == FALSE & "POSIXct" %in% class(DatesR) == FALSE) {
-        stop("DatesR must be defined as POSIXlt or POSIXct \n")
-        return(NULL)
-      }
-      if ("POSIXlt" %in% class(DatesR) == FALSE) {
-        DatesR <- as.POSIXlt(DatesR)
-      }
-      if (difftime(tail(DatesR, 1), tail(DatesR, 2), units = "secs")[[1]] %in% TimeStep == FALSE) {
-        TimeStepName <- grep("hourly|daily|monthly|yearly", ObjectClass, value = TRUE)
-        stop(paste0("The time step of the model inputs must be ", TimeStepName, "\n"))
-        return(NULL)
-      }
-      if (any(duplicated(DatesR))) {
-        stop("DatesR must not include duplicated values \n")
-        return(NULL)
-      }
-      LLL <- length(DatesR)
+
+
+  ObjectClass <- NULL
+
+  ## check DatesR
+  if (is.null(DatesR)) {
+    stop("'DatesR' is missing")
+  }
+  if (!"POSIXlt" %in% class(DatesR) & !"POSIXct" %in% class(DatesR)) {
+    stop("'DatesR' must be defined as 'POSIXlt' or 'POSIXct'")
+  }
+  if (!"POSIXlt" %in% class(DatesR)) {
+    DatesR <- as.POSIXlt(DatesR)
+  }
+  if (any(duplicated(DatesR))) {
+    stop("'DatesR' must not include duplicated values")
+  }
+  LLL <- length(DatesR)
+
+  ## check FUN_MOD
+  FUN_MOD <- match.fun(FUN_MOD)
+  FeatFUN_MOD <- .GetFeatModel(FUN_MOD = FUN_MOD, DatesR = DatesR)
+  ObjectClass <- FeatFUN_MOD$Class
+  TimeStep <- FeatFUN_MOD$TimeStep
+
+
+  ##check_arguments
+
+  if ("GR" %in% ObjectClass) {
+    if (is.null(Precip)) {
+      stop("Precip is missing")
     }
-    if ("GR" %in% ObjectClass) {
-      if (is.null(Precip)) {
-        stop("Precip is missing \n")
-        return(NULL)
-      }
-      if (is.null(PotEvap)) {
-        stop("PotEvap is missing \n")
-        return(NULL)
-      }
-      if (!is.vector(Precip) | !is.vector(PotEvap)) {
-        stop("Precip and PotEvap must be vectors of numeric values \n")
-        return(NULL)
-      }
-      if (!is.numeric(Precip) | !is.numeric(PotEvap)) {
-        stop("Precip and PotEvap must be vectors of numeric values \n")
-        return(NULL)
-      }
-      if (length(Precip) != LLL | length(PotEvap) != LLL) {
-        stop("Precip, PotEvap and DatesR must have the same length \n")
-        return(NULL)
-      }
+    if (is.null(PotEvap)) {
+      stop("'PotEvap' is missing")
     }
-    if ("CemaNeige" %in% ObjectClass) {
-      if (is.null(Precip)) {
-        stop("Precip is missing \n")
-        return(NULL)
+    if (!is.vector(Precip) | !is.vector(PotEvap)) {
+      stop("'Precip' and 'PotEvap' must be vectors of numeric values")
+    }
+    if (!is.numeric(Precip) | !is.numeric(PotEvap)) {
+      stop("'Precip' and 'PotEvap' must be vectors of numeric values")
+    }
+    if (length(Precip) != LLL | length(PotEvap) != LLL) {
+      stop("'Precip', 'PotEvap' and 'DatesR' must have the same length")
+    }
+  }
+  if ("CemaNeige" %in% ObjectClass) {
+    if (is.null(Precip)) {
+      stop("'Precip' is missing")
+    }
+    if (is.null(TempMean)) {
+      stop("'TempMean' is missing")
+    }
+    if (!is.vector(Precip) | !is.vector(TempMean)) {
+      stop("'Precip' and 'TempMean' must be vectors of numeric values")
+    }
+    if (!is.numeric(Precip) | !is.numeric(TempMean)) {
+      stop("'Precip' and 'TempMean' must be vectors of numeric values")
+    }
+    if (length(Precip) != LLL | length(TempMean) != LLL) {
+      stop("'Precip', 'TempMean' and 'DatesR' must have the same length")
+    }
+    if (is.null(TempMin) != is.null(TempMax)) {
+      stop("'TempMin' and 'TempMax' must be both defined if not null")
+    }
+    if (!is.null(TempMin) & !is.null(TempMax)) {
+      if (!is.vector(TempMin) | !is.vector(TempMax)) {
+        stop("'TempMin' and 'TempMax' must be vectors of numeric values")
       }
-      if (is.null(TempMean)) {
-        stop("TempMean is missing \n")
-        return(NULL)
+      if (!is.numeric(TempMin) | !is.numeric(TempMax)) {
+        stop("'TempMin' and 'TempMax' must be vectors of numeric values")
       }
-      if (!is.vector(Precip) | !is.vector(TempMean)) {
-        stop("Precip and TempMean must be vectors of numeric values \n")
-        return(NULL)
+      if (length(TempMin) != LLL | length(TempMax) != LLL) {
+        stop("'TempMin', 'TempMax' and 'DatesR' must have the same length")
       }
-      if (!is.numeric(Precip) | !is.numeric(TempMean)) {
-        stop("Precip and TempMean must be vectors of numeric values \n")
-        return(NULL)
+    }
+    if (!is.null(HypsoData)) {
+      if (!is.vector(HypsoData)) {
+        stop("'HypsoData' must be a vector of numeric values  if not null")
       }
-      if (length(Precip) != LLL | length(TempMean) != LLL) {
-        stop("Precip, TempMean and DatesR must have the same length \n")
-        return(NULL)
+      if (!is.numeric(HypsoData)) {
+        stop("'HypsoData' must be a vector of numeric values  if not null")
       }
-      if (is.null(TempMin) != is.null(TempMax)) {
-        stop("TempMin and TempMax must be both defined if not null \n")
-        return(NULL)
+      if (length(HypsoData) != 101) {
+        stop("'HypsoData' must be of length 101 if not null")
       }
-      if (!is.null(TempMin) & !is.null(TempMax)) {
-        if (!is.vector(TempMin) | !is.vector(TempMax)) {
-          stop("TempMin and TempMax must be vectors of numeric values \n")
-          return(NULL)
-        }
-        if (!is.numeric(TempMin) | !is.numeric(TempMax)) {
-          stop("TempMin and TempMax must be vectors of numeric values \n")
-          return(NULL)
-        }
-        if (length(TempMin) != LLL | length(TempMax) != LLL) {
-          stop("TempMin, TempMax and DatesR must have the same length \n")
-          return(NULL)
-        }
+      if (sum(is.na(HypsoData)) != 0 & sum(is.na(HypsoData)) != 101) {
+        stop("'HypsoData' must not contain any NA if not null")
       }
-      if (!is.null(HypsoData)) {
-        if (!is.vector(HypsoData)) {
-          stop("HypsoData must be a vector of numeric values  if not null \n")
-          return(NULL)
-        }
-        if (!is.numeric(HypsoData)) {
-          stop("HypsoData must be a vector of numeric values  if not null \n")
-          return(NULL)
-        }
-        if (length(HypsoData) != 101) {
-          stop("HypsoData must be of length 101 if not null \n")
-          return(NULL)
-        }
-        if (sum(is.na(HypsoData)) != 0 & sum(is.na(HypsoData)) != 101) {
-          stop("HypsoData must not contain any NA if not null \n")
-          return(NULL)
-        }
+    }
+    if (!is.null(ZInputs)) {
+      if (length(ZInputs) != 1) {
+        stop("'ZInputs' must be a single numeric value if not null")
       }
-      if (!is.null(ZInputs)) {
-        if (length(ZInputs) != 1) {
-          stop("\t ZInputs must be a single numeric value if not null \n")
-          return(NULL)
-        }
-        if (is.na(ZInputs) | !is.numeric(ZInputs)) {
-          stop("\t ZInputs must be a single numeric value if not null \n")
-          return(NULL)
-        }
+      if (is.na(ZInputs) | !is.numeric(ZInputs)) {
+        stop("'ZInputs' must be a single numeric value if not null")
       }
-      if (is.null(HypsoData)) {
-        if (verbose) {
-          warning("\t HypsoData is missing => a single layer is used and no extrapolation is made \n")
-        }
-        HypsoData <- as.numeric(rep(NA, 101))
-        ZInputs   <- as.numeric(NA)
-        NLayers   <- as.integer(1)
-        
+    }
+    if (is.null(HypsoData)) {
+      if (verbose) {
+        warning("'HypsoData' is missing: a single layer is used and no extrapolation is made", call. = FALSE)
       }
-      if (is.null(ZInputs)) {
-        if (verbose & !identical(HypsoData, as.numeric(rep(NA, 101)))) {
-          warning("\t ZInputs is missing => HypsoData[51] is used \n")
-        }
-        ZInputs <- HypsoData[51L]
+      HypsoData <- as.numeric(rep(NA, 101))
+      ZInputs   <- as.numeric(NA)
+      NLayers   <- as.integer(1)
+
+    }
+    if (is.null(ZInputs)) {
+      if (verbose & !identical(HypsoData, as.numeric(rep(NA, 101)))) {
+        warning("'ZInputs' is missing: HypsoData[51] is used")
       }
-      if (NLayers <= 0) {
-        stop("NLayers must be a positive integer value \n")
-        return(NULL)
+      ZInputs <- HypsoData[51L]
+    }
+    if (NLayers <= 0) {
+      stop("'NLayers' must be a positive integer value")
+    }
+    if (NLayers != as.integer(NLayers)) {
+      warning("Coerce 'NLayers' to be of integer type (",  NLayers, ": ", as.integer(NLayers), ")")
+      NLayers <- as.integer(NLayers)
+    }
+  }
+
+  ## check semi-distributed mode
+  if (!is.null(Qupstream) & !is.null(LengthHydro) & !is.null(BasinAreas)) {
+    ObjectClass <- c(ObjectClass, "SD")
+  } else if (verbose & !all(c(is.null(Qupstream), is.null(LengthHydro), is.null(BasinAreas)))) {
+    warning("Missing argument: 'Qupstream', 'LengthHydro' and 'BasinAreas' must all be set to run in a semi-distributed mode. The lumped mode will be used")
+  }
+  if ("SD" %in% ObjectClass) {
+    if (!("daily" %in% ObjectClass) & !("hourly" %in% ObjectClass)) {
+      stop("Only daily and hourly time steps can be used in a semi-distributed mode")
+    }
+    if (!is.matrix(Qupstream) | !is.numeric(Qupstream)) {
+      stop("'Qupstream' must be a matrice of numeric values")
+    }
+    if (!is.vector(LengthHydro) | !is.vector(BasinAreas) | !is.numeric(LengthHydro) | !is.numeric(BasinAreas)) {
+      stop("'LengthHydro' and 'BasinAreas' must be vectors of numeric values")
+    }
+    if (ncol(Qupstream) != length(LengthHydro)) {
+      stop("'Qupstream' number of columns and 'LengthHydro' length must be equal")
+    }
+    if (length(LengthHydro) + 1 != length(BasinAreas)) {
+      stop("'BasinAreas' must have one more element than 'LengthHydro'")
+    }
+    if (nrow(Qupstream) != LLL) {
+      stop("'Qupstream' must have same number of rows as 'DatesR' length")
+    }
+    if (any(is.na(Qupstream))) {
+      warning("'Qupstream' contains NA values: model outputs will contain NAs")
+    }
+    if (any(LengthHydro > 1000)) {
+      warning("The unit of 'LengthHydro' has changed from m to km in airGR >= 1.6.12: values superior to 1000 km seem unrealistic")
+    }
+    QupstrUnit <- tolower(QupstrUnit)
+    QupstrUnit <- match.arg(arg = QupstrUnit, choices = c("mm", "m3", "m3/s", "l/s"))
+  }
+
+  ##check_NA_values
+  BOOL_NA <- rep(FALSE, length(DatesR))
+
+  if ("GR" %in% ObjectClass) {
+    BOOL_NA_TMP <- (Precip  < 0) | is.na(Precip)
+    if (sum(BOOL_NA_TMP) != 0) {
+      BOOL_NA <- BOOL_NA |  BOOL_NA_TMP
+      if (verbose) {
+        warning("Values < 0 or NA values detected in 'Precip' series")
       }
-      if (NLayers != as.integer(NLayers)) {
-        warning("Coerce NLayers to be of integer type (",  NLayers, " => ", as.integer(NLayers), ")")
-        NLayers <- as.integer(NLayers)
+    }
+    BOOL_NA_TMP <- (PotEvap < 0) | is.na(PotEvap)
+    if (sum(BOOL_NA_TMP) != 0) {
+      BOOL_NA <- BOOL_NA | BOOL_NA_TMP
+      if (verbose) {
+        warning("Values < 0 or NA values detected in 'PotEvap' series")
       }
     }
-    
-    
-    ##check_NA_values
-    BOOL_NA <- rep(FALSE, length(DatesR))
-    
-    if ("GR" %in% ObjectClass) {
-      BOOL_NA_TMP <- (Precip  < 0) | is.na(Precip)
-      if (sum(BOOL_NA_TMP) != 0) {
-        BOOL_NA <- BOOL_NA |  BOOL_NA_TMP
-        if (verbose) {
-          warning("\t Values < 0 or NA values detected in Precip series  \n")
-        }
+  }
+  if ("CemaNeige" %in% ObjectClass) {
+    BOOL_NA_TMP <- (Precip  < 0) | is.na(Precip)
+    if (sum(BOOL_NA_TMP) != 0) {
+      BOOL_NA <- BOOL_NA | BOOL_NA_TMP
+      if (verbose) {
+        warning("Values < 0 or NA values detected in 'Precip' series")
       }
-      BOOL_NA_TMP <- (PotEvap < 0) | is.na(PotEvap)
-      if (sum(BOOL_NA_TMP) != 0) {
-        BOOL_NA <- BOOL_NA | BOOL_NA_TMP
-        if (verbose) {
-          warning("\t Values < 0 or NA values detected in PotEvap series \n")
-        }
+    }
+    BOOL_NA_TMP <- (TempMean < (-150)) | is.na(TempMean)
+    if (sum(BOOL_NA_TMP) != 0) {
+      BOOL_NA <- BOOL_NA | BOOL_NA_TMP
+      if (verbose) {
+        warning("Values < -150 or NA values detected in 'TempMean' series")
       }
     }
-    if ("CemaNeige" %in% ObjectClass) {
-      BOOL_NA_TMP <- (Precip  < 0) | is.na(Precip)
+    if (!is.null(TempMin) & !is.null(TempMax)) {
+      BOOL_NA_TMP <- (TempMin < (-150)) | is.na(TempMin)
       if (sum(BOOL_NA_TMP) != 0) {
         BOOL_NA <- BOOL_NA | BOOL_NA_TMP
         if (verbose) {
-          warning("\t Values < 0 or NA values detected in Precip series       \n")
+          warning("Values < -150 or NA values detected in 'TempMin' series")
         }
       }
-      BOOL_NA_TMP <-  (TempMean < (-150)) | is.na(TempMean)
+      BOOL_NA_TMP <- (TempMax < (-150)) | is.na(TempMax)
       if (sum(BOOL_NA_TMP) != 0) {
         BOOL_NA <- BOOL_NA | BOOL_NA_TMP
         if (verbose) {
-          warning("\t Values < -150) or NA values detected in TempMean series \n")
+          warning("Values < -150 or NA values detected in 'TempMax' series")
         }
       }
+    }
+  }
+  if (sum(BOOL_NA) != 0) {
+    WTxt <- NULL
+    WTxt <- paste(WTxt, "\t Missing values are not allowed in 'InputsModel'", sep = "")
+
+    Select <- (max(which(BOOL_NA)) + 1):length(BOOL_NA)
+
+    if (Select[1L] > Select[2L]) {
+      stop("time series could not be trunced since missing values were detected at the last time-step")
+    }
+    if ("GR" %in% ObjectClass) {
+      Precip  <- Precip[Select]
+      PotEvap <- PotEvap[Select]
+    }
+    if ("CemaNeige" %in% ObjectClass) {
+      Precip   <- Precip[Select]
+      TempMean <- TempMean[Select]
       if (!is.null(TempMin) & !is.null(TempMax)) {
-        BOOL_NA_TMP <- (TempMin < (-150)) | is.na(TempMin)
-        if (sum(BOOL_NA_TMP) != 0) {
-          BOOL_NA <- BOOL_NA | BOOL_NA_TMP
-          if (verbose) {
-            warning("\t Values < -150) or NA values detected in TempMin series \n")
-          }
-        }
-        BOOL_NA_TMP <-  (TempMax < (-150)) | is.na(TempMax)
-        if (sum(BOOL_NA_TMP) != 0) {
-          BOOL_NA <- BOOL_NA | BOOL_NA_TMP
-          if (verbose) {
-            warning("\t Values < -150) or NA values detected in TempMax series \n")
-          }
-        }
+        TempMin <- TempMin[Select]
+        TempMax <- TempMax[Select]
       }
     }
-    if (sum(BOOL_NA) != 0) {
-      WTxt <- NULL
-      WTxt <- paste(WTxt, "\t Missing values are not allowed in InputsModel \n", sep = "")
-      
-      Select <- (max(which(BOOL_NA)) + 1):length(BOOL_NA)
-      
-      if (Select[1L] > Select[2L]) {
-        stop("Time series could not be trunced since missing values were detected at the list time-step")
-        return(NULL)
-      }
-      if ("GR" %in% ObjectClass) {
-        Precip  <- Precip[Select]
-        PotEvap <- PotEvap[Select]
-      }
-      if ("CemaNeige" %in% ObjectClass) {
-        Precip   <- Precip[Select]
-        TempMean <- TempMean[Select]
-        if (!is.null(TempMin) & !is.null(TempMax)) {
-          TempMin <- TempMin[Select]
-          TempMax <- TempMax[Select]
-        }
-      }
-      
-      DatesR <- DatesR[Select]
-      
-      WTxt <- paste(WTxt, "\t -> Data were trunced to keep the most recent available time-steps \n", sep = "")
-      WTxt <- paste(WTxt, "\t -> ", length(Select), " time-steps were kept \n", sep = "")
-      
-      if (!is.null(WTxt) & verbose) {
-        warning(WTxt)
-      }
+
+    DatesR <- DatesR[Select]
+
+    WTxt <- paste0(WTxt, "\t -> data were trunced to keep the most recent available time-steps")
+    WTxt <- paste0(WTxt, "\t -> ", length(Select), " time-steps were kept")
+
+    if (!is.null(WTxt) & verbose) {
+      warning(WTxt)
     }
-    
-    
-    ##DataAltiExtrapolation_Valery
-    if ("CemaNeige" %in% ObjectClass) {
-      RESULT <- DataAltiExtrapolation_Valery(DatesR = DatesR,
-                                             Precip = Precip, PrecipScale = PrecipScale,
-                                             TempMean = TempMean, TempMin = TempMin, TempMax = TempMax,
-                                             ZInputs = ZInputs, HypsoData = HypsoData, NLayers = NLayers,
-                                             verbose = verbose)
-      if (verbose) {
-        if (NLayers == 1) {
-          message("\t Input series were successfully created on 1 elevation layer for use by CemaNeige")
-        } else {
-          message( "\t Input series were successfully created on ", NLayers, " elevation layers for use by CemaNeige")
-        }
+  }
+
+
+  ##DataAltiExtrapolation_Valery
+  if ("CemaNeige" %in% ObjectClass) {
+    RESULT <- DataAltiExtrapolation_Valery(DatesR = DatesR,
+                                           Precip = Precip, PrecipScale = PrecipScale,
+                                           TempMean = TempMean, TempMin = TempMin, TempMax = TempMax,
+                                           ZInputs = ZInputs, HypsoData = HypsoData, NLayers = NLayers,
+                                           verbose = verbose)
+    if (verbose) {
+      if (NLayers == 1) {
+        message("input series were successfully created on 1 elevation layer for use by CemaNeige")
+      } else {
+        message( "input series were successfully created on ", NLayers, " elevation layers for use by CemaNeige")
       }
     }
-    
-    
-    ##Create_InputsModel
-    InputsModel <- list(DatesR = DatesR)
-    if ("GR" %in% ObjectClass) {
-      InputsModel <- c(InputsModel, list(Precip = as.double(Precip), PotEvap = as.double(PotEvap)))
+  }
+
+
+  ##Create_InputsModel
+  InputsModel <- list(DatesR = DatesR)
+  if ("GR" %in% ObjectClass) {
+    InputsModel <- c(InputsModel, list(Precip = as.double(Precip), PotEvap = as.double(PotEvap)))
+  }
+  if ("CemaNeige" %in% ObjectClass) {
+    InputsModel <- c(InputsModel, list(LayerPrecip          = RESULT$LayerPrecip,
+                                       LayerTempMean        = RESULT$LayerTempMean,
+                                       LayerFracSolidPrecip = RESULT$LayerFracSolidPrecip,
+                                       ZLayers              = RESULT$ZLayers))
+  }
+  if ("SD" %in% ObjectClass) {
+    # Qupstream is internally stored in m3/time step
+    if (QupstrUnit == "mm") {
+      iConvBasins <- which(!is.na(BasinAreas[seq.int(length(LengthHydro))]))
+      Qupstream[, iConvBasins] <- Qupstream[, iConvBasins] * rep(BasinAreas[iConvBasins], each = LLL) * 1e3
+    } else if (QupstrUnit == "m3/s") {
+      Qupstream <- Qupstream * TimeStep
+    } else if (QupstrUnit == "l/s") {
+      Qupstream <- Qupstream * TimeStep / 1e3
     }
-    if ("CemaNeige" %in% ObjectClass) {
-      InputsModel <- c(InputsModel, list(LayerPrecip          = RESULT$LayerPrecip,
-                                         LayerTempMean        = RESULT$LayerTempMean,
-                                         LayerFracSolidPrecip = RESULT$LayerFracSolidPrecip,
-                                         ZLayers              = RESULT$ZLayers))
-    }
-    
-    class(InputsModel) <- c("InputsModel", ObjectClass)
-    
-    return(InputsModel)
-    
-    
-    
+    InputsModel <- c(InputsModel, list(Qupstream = Qupstream,
+                                       LengthHydro = LengthHydro,
+                                       BasinAreas = BasinAreas))
   }
+
+  class(InputsModel) <- c("InputsModel", ObjectClass)
+
+  return(InputsModel)
+
+
+
+}

R/CreateRunOptions.R

-CreateRunOptions <- function(FUN_MOD, InputsModel, IndPeriod_WarmUp = NULL, IndPeriod_Run, IniStates = NULL, IniResLevels = NULL, 
-                             Outputs_Cal = NULL, Outputs_Sim = "all", RunSnowModule, MeanAnSolidPrecip = NULL,  verbose = TRUE) {
-  
-  if (!missing(RunSnowModule)) {
-    warning("argument RunSnowModule is deprecated; please adapt FUN_MOD instead.", call. = FALSE)
-  }
-  
-  ObjectClass <- NULL
-  
-  ##check_FUN_MOD
-  BOOL <- FALSE;
-  if (identical(FUN_MOD, RunModel_GR4H)) {
-    ObjectClass <- c(ObjectClass, "GR", "hourly")
-    BOOL <- TRUE
-  }
-  if (identical(FUN_MOD, RunModel_GR4J) | identical(FUN_MOD, RunModel_GR5J) | identical(FUN_MOD, RunModel_GR6J)) {
-    ObjectClass <- c(ObjectClass, "GR", "daily")
-    BOOL <- TRUE
-  }
-  if (identical(FUN_MOD, RunModel_GR2M)) {
-    ObjectClass <- c(ObjectClass, "GR", "monthly")
-    BOOL <- TRUE
-  }
-  if (identical(FUN_MOD, RunModel_GR1A)) {
-    ObjectClass <- c(ObjectClass, "GR", "yearly")
-    BOOL <- TRUE
-  }
-  if (identical(FUN_MOD, RunModel_CemaNeige)) {
-    ObjectClass <- c(ObjectClass, "CemaNeige", "daily")
-    BOOL <- TRUE
-  }
-  if (identical(FUN_MOD, RunModel_CemaNeigeGR4J) | identical(FUN_MOD, RunModel_CemaNeigeGR5J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J)) {
-    ObjectClass <- c(ObjectClass, "GR", "CemaNeige", "daily")
-    BOOL <- TRUE
-  }
-  if (!BOOL) {
-    stop("incorrect FUN_MOD for use in CreateRunOptions \n")
-    return(NULL)
-  }
-  
+CreateRunOptions <- function(FUN_MOD, InputsModel,
+                             IndPeriod_WarmUp = NULL, IndPeriod_Run,
+                             IniStates = NULL, IniResLevels = NULL, Imax = NULL,
+                             Outputs_Cal = NULL, Outputs_Sim = "all",
+                             MeanAnSolidPrecip = NULL, IsHyst = FALSE,
+                             warnings = TRUE, verbose = TRUE) {
+
+  if (!is.null(Imax)) {
+    if (!is.numeric(Imax) | length(Imax) != 1L) {
+      stop("'Imax' must be a non negative 'numeric' value of length 1")
+    } else {
+      if (Imax < 0) {
+        stop("'Imax' must be a non negative 'numeric' value of length 1")
+      }
+    }
+    IsIntStore <- TRUE
+  } else {
+    IsIntStore <- FALSE
+  }
+
+  ## check FUN_MOD
+  FUN_MOD <- match.fun(FUN_MOD)
+  FeatFUN_MOD <- .GetFeatModel(FUN_MOD = FUN_MOD, DatesR = InputsModel$DatesR)
+  ObjectClass <- FeatFUN_MOD$Class
+  TimeStepMean <- FeatFUN_MOD$TimeStepMean
+
+  ## Model output variable list
+  FortranOutputs <- .FortranOutputs(GR = FeatFUN_MOD$CodeModHydro,
+                                    isCN = "CemaNeige" %in% FeatFUN_MOD$Class)
+
+  ## manage class
+  if (IsIntStore) {
+    ObjectClass <- c(ObjectClass, "interception")
+  }
+  if ("CemaNeige" %in% FeatFUN_MOD$Class) {
+    FeatFUN_MOD$IsHyst <- IsHyst
+    if (IsHyst) {
+      ObjectClass <- c(ObjectClass, "hysteresis")
+      FeatFUN_MOD$NbParam <- FeatFUN_MOD$NbParam + 2
+    }
+  }
+
+  ## SD model
+  FeatFUN_MOD$IsSD <- inherits(InputsModel, "SD")
+  if (FeatFUN_MOD$IsSD) {
+    FeatFUN_MOD$NbParam <- FeatFUN_MOD$NbParam + 1
+  }
+
+  if (!"CemaNeige" %in% ObjectClass & "hysteresis" %in% ObjectClass) {
+    stop("'IsHyst' cannot be TRUE for the chosen 'FUN_MOD'")
+  }
+  if (!(identical(FUN_MOD, RunModel_GR5H) | identical(FUN_MOD, RunModel_CemaNeigeGR5H)) & "interception" %in% ObjectClass) {
+    stop("'IMax' cannot be set for the chosen 'FUN_MOD'")
+  }
+
   ##check_InputsModel
   if (!inherits(InputsModel, "InputsModel")) {
-    stop("InputsModel must be of class 'InputsModel' \n")
-    return(NULL)
+    stop("'InputsModel' must be of class 'InputsModel'")
   }
   if ("GR" %in% ObjectClass & !inherits(InputsModel, "GR")) {
-    stop("InputsModel must be of class 'GR' \n")
-    return(NULL)
+    stop("'InputsModel' must be of class 'GR'")
   }
   if ("CemaNeige" %in% ObjectClass &
       !inherits(InputsModel, "CemaNeige")) {
-    stop("InputsModel must be of class 'CemaNeige' \n")
-    return(NULL)
+    stop("'InputsModel' must be of class 'CemaNeige'")
   }
   if ("hourly" %in% ObjectClass &
       !inherits(InputsModel, "hourly")) {
-    stop("InputsModel must be of class 'hourly' \n")
-    return(NULL)
+    stop("'InputsModel' must be of class 'hourly'")
   }
   if ("daily" %in% ObjectClass & !inherits(InputsModel, "daily")) {
-    stop("InputsModel must be of class 'daily' \n")
-    return(NULL)
+    stop("'InputsModel' must be of class 'daily'")
   }
   if ("monthly" %in% ObjectClass &
       !inherits(InputsModel, "monthly")) {
-    stop("InputsModel must be of class 'monthly' \n")
-    return(NULL)
+    stop("'InputsModel' must be of class 'monthly'")
   }
   if ("yearly" %in% ObjectClass &
       !inherits(InputsModel, "yearly")) {
-    stop("InputsModel must be of class 'yearly' \n")
-    return(NULL)
+    stop("'InputsModel' must be of class 'yearly'")
   }
-  
-  
+
+
   ##check_IndPeriod_Run
   if (!is.vector(IndPeriod_Run)) {
-    stop("IndPeriod_Run must be a vector of numeric values \n")
-    return(NULL)
+    stop("'IndPeriod_Run' must be a vector of numeric values")
   }
   if (!is.numeric(IndPeriod_Run)) {
-    stop("IndPeriod_Run must be a vector of numeric values \n")
-    return(NULL)
+    stop("'IndPeriod_Run' must be a vector of numeric values")
   }
-  if (identical(as.integer(IndPeriod_Run), as.integer(seq(from = IndPeriod_Run[1], to = tail(IndPeriod_Run, 1), by = 1))) == FALSE) {
-    stop("IndPeriod_Run must be a continuous sequence of integers \n")
-    return(NULL)
+  if (!identical(as.integer(IndPeriod_Run), as.integer(seq(from = IndPeriod_Run[1], to = tail(IndPeriod_Run, 1), by = 1)))) {
+    stop("'IndPeriod_Run' must be a continuous sequence of integers")
   }
   if (storage.mode(IndPeriod_Run) != "integer") {
-    stop("IndPeriod_Run should be of type integer \n")
-    return(NULL)
+    stop("'IndPeriod_Run' should be of type integer")
   }
-  
-  
+
+
   ##check_IndPeriod_WarmUp
   WTxt <- NULL
   if (is.null(IndPeriod_WarmUp)) {
-    WTxt <- paste0(WTxt,"\t Model warm up period not defined -> default configuration used \n")
+    WTxt <- paste(WTxt, "model warm up period not defined: default configuration used", sep = "")
     ##If_the_run_period_starts_at_the_very_beginning_of_the_time_series
-    if (IndPeriod_Run[1] == as.integer(1)) {
-      IndPeriod_WarmUp <- as.integer(0)
-      WTxt <- paste0(WTxt,"\t    No data were found for model warm up! \n")
+    if (IndPeriod_Run[1L] == 1L) {
+      IndPeriod_WarmUp <- 0L
+      WTxt <- paste0(WTxt,"\n no data were found for model warm up!")
       ##We_look_for_the_longest_period_preceeding_the_run_period_with_a_maximum_of_one_year
     } else {
       TmpDateR0 <- InputsModel$DatesR[IndPeriod_Run[1]]
@@ -110,90 +114,109 @@ CreateRunOptions <- function(FUN_MOD, InputsModel, IndPeriod_WarmUp = NULL, IndP
         TmpDateR <- TmpDateR - 1 * 24 * 60 * 60
       }
       IndPeriod_WarmUp <- which(InputsModel$DatesR == max(InputsModel$DatesR[1], TmpDateR)):(IndPeriod_Run[1] - 1)
-      if ("hourly"  %in% ObjectClass) {
-        TimeStep <- as.integer(60 * 60)
-      }
-      if ("daily"   %in% ObjectClass) {
-        TimeStep <- as.integer(24 * 60 * 60)
-      }
-      if ("monthly" %in% ObjectClass) {
-        TimeStep <- as.integer(30.44 * 24 * 60 * 60)
-      }
-      if ("yearly"  %in% ObjectClass) {
-        TimeStep <- as.integer(365.25 * 24 * 60 * 60)
-      }
-      if (length(IndPeriod_WarmUp) * TimeStep / (365 * 24 * 60 * 60) >= 1) {
-        WTxt <- paste0(WTxt, "\t    The year preceding the run period is used \n")
+      if (length(IndPeriod_WarmUp) * TimeStepMean / (365 * 24 * 60 * 60) >= 1) {
+        WTxt <- paste0(WTxt, "\n  the year preceding the run period is used \n")
       } else {
-        WTxt <- paste0(WTxt, "\t    Less than a year (without missing values) was found for model warm up: \n")
-        WTxt <- paste0(WTxt, "\t    (", length(IndPeriod_WarmUp), " time-steps are used for initialisation) \n")
+        WTxt <- paste0(WTxt, "\n  less than a year (without missing values) was found for model warm up:")
+        WTxt <- paste0(WTxt, "\n  (", length(IndPeriod_WarmUp), " time-steps are used for initialisation)")
       }
     }
   }
   if (!is.null(IndPeriod_WarmUp)) {
     if (!is.vector(IndPeriod_WarmUp)) {
-      stop("IndPeriod_Run must be a vector of numeric values \n")
-      return(NULL)
+      stop("'IndPeriod_WarmUp' must be a vector of numeric values")
     }
     if (!is.numeric(IndPeriod_WarmUp)) {
-      stop("IndPeriod_Run must be a vector of numeric values \n")
-      return(NULL)
+      stop("'IndPeriod_WarmUp' must be a vector of numeric values")
     }
     if (storage.mode(IndPeriod_WarmUp) != "integer") {
-      stop("IndPeriod_Run should be of type integer \n")
-      return(NULL)
+      stop("'IndPeriod_WarmUp' should be of type integer")
     }
-    if (identical(IndPeriod_WarmUp, as.integer(0))) {
-      WTxt <- paste0(WTxt, "\t No warm up period is used! \n")
+    if (identical(IndPeriod_WarmUp, 0L) & verbose) {
+      message(paste0(WTxt, " No warm up period is used"))
     }
-    if ((IndPeriod_Run[1] - 1) != tail(IndPeriod_WarmUp, 1) & !identical(IndPeriod_WarmUp, as.integer(0))) {
-      WTxt <- paste0(WTxt, "\t Model warm up period is not directly before the model run period \n")
+    if ((IndPeriod_Run[1] - 1) != tail(IndPeriod_WarmUp, 1) & !identical(IndPeriod_WarmUp, 0L)) {
+      WTxt <- paste0(WTxt, " Model warm up period is not directly before the model run period")
     }
   }
-  if (!is.null(WTxt) & verbose) {
+  if (!is.null(WTxt) & warnings) {
     warning(WTxt)
-    
   }
-  
-  
-  ## check IniResLevels    
+
+
+  ## check IniResLevels
   if ("GR" %in% ObjectClass & ("monthly" %in% ObjectClass | "daily" %in% ObjectClass | "hourly" %in% ObjectClass)) {
     if (!is.null(IniResLevels)) {
-      if (!is.vector(IniResLevels) | !is.numeric(IniResLevels) | any(is.na(IniResLevels))) {
-        stop("IniResLevels must be a vector of numeric values \n")
-        return(NULL)
+      # if (!is.vector(IniResLevels) | !is.numeric(IniResLevels) | any(is.na(IniResLevels))) {
+      if (!is.vector(IniResLevels) | is.character(IniResLevels) | is.factor(IniResLevels) | length(IniResLevels) != 4) {
+        stop("'IniResLevels' must be a vector of 4 numeric values")
       }
-      if ((identical(FUN_MOD, RunModel_GR4H) |
-           identical(FUN_MOD, RunModel_GR4J) | identical(FUN_MOD, RunModel_CemaNeigeGR4J) |
-           identical(FUN_MOD, RunModel_GR5J) | identical(FUN_MOD, RunModel_CemaNeigeGR5J) |
-           identical(FUN_MOD, RunModel_GR2M)) &
-          length(IniResLevels) != 2) {
-        stop("The length of IniResLevels must be 2 for the chosen FUN_MOD \n")
-        return(NULL)
+      # if ((identical(FUN_MOD, RunModel_GR4H) | identical(FUN_MOD, RunModel_CemaNeigeGR4H) |
+      #      # (identical(FUN_MOD, RunModel_GR5H) & !IsIntStore) |
+      #      identical(FUN_MOD, RunModel_GR5H) |
+      #      identical(FUN_MOD, RunModel_GR4J) | identical(FUN_MOD, RunModel_CemaNeigeGR4J) |
+      #      identical(FUN_MOD, RunModel_GR5J) | identical(FUN_MOD, RunModel_CemaNeigeGR5J) |
+      #      identical(FUN_MOD, RunModel_GR2M)) &
+      #     length(IniResLevels) != 2) {
+      #   stop("the length of 'IniResLevels' must be 2 for the chosen 'FUN_MOD'")
+      # }
+      if (any(is.na(IniResLevels[1:2]))) {
+        stop("the first 2 values of 'IniResLevels' cannot be missing values for the chosen 'FUN_MOD'")
+      }
+      # if ((identical(FUN_MOD, RunModel_GR6J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J) |
+      #      (identical(FUN_MOD, RunModel_GR5H) & IsIntStore)) &
+      #     length(IniResLevels) != 3) {
+      #   stop("the length of 'IniResLevels' must be 3 for the chosen 'FUN_MOD'")
+      # }
+      if ((identical(FUN_MOD, RunModel_GR6J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J))) {
+        if (is.na(IniResLevels[3L])) {
+          stop("the third value of 'IniResLevels' cannot be a missing value for the chosen 'FUN_MOD'")
+        }
+      } else {
+        if (!is.na(IniResLevels[3L])) {
+          warning("the third value of 'IniResLevels' is set to NA value for the chosen 'FUN_MOD'. Only GR6J presents an exponential store")
+          IniResLevels[3L] <- NA
+        }
       }
-      if ((identical(FUN_MOD,RunModel_GR6J) | identical(FUN_MOD,RunModel_CemaNeigeGR6J)) &
-          length(IniResLevels) != 3) {
-        stop("The length of IniResLevels must be 3 for the chosen FUN_MOD \n")
-        return(NULL)
+      if (identical(FUN_MOD, RunModel_GR5H) | identical(FUN_MOD, RunModel_CemaNeigeGR5H)) {
+        if (IsIntStore & is.na(IniResLevels[4L])) {
+          stop("the fourth value of 'IniResLevels' cannot be a missing value for the chosen 'FUN_MOD' (GR5H with an interception store)")
+        }
+        if (!IsIntStore & !is.na(IniResLevels[4L])) {
+          warning("the fourth value of 'IniResLevels' is set to NA value for the chosen 'FUN_MOD'. Only GR5H used with an 'Imax' value presents an interception store")
+          IniResLevels[4L] <- NA
+        }
+      } else {
+        if (!is.na(IniResLevels[4L])) {
+          warning("the fourth value of 'IniResLevels' is set to NA value for the chosen 'FUN_MOD'. Only GR5H used with an 'Imax' value presents an interception store")
+          IniResLevels[4L] <- NA
+        }
       }
     } else if (is.null(IniStates)) {
+      IniResLevels <- as.double(c(0.3, 0.5, NA, NA))
       if (identical(FUN_MOD, RunModel_GR6J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J)) {
-        IniResLevels <- as.double(c(0.3, 0.5, 0))
-      } else {
-        IniResLevels <- as.double(c(0.3, 0.5, NA))
+        IniResLevels <- as.double(c(0.3, 0.5, 0, NA))
+      }
+      if ((identical(FUN_MOD, RunModel_GR5H) | identical(FUN_MOD, RunModel_CemaNeigeGR5H)) & IsIntStore) {
+        IniResLevels <- as.double(c(0.3, 0.5, NA, 0))
       }
+      # if (!identical(FUN_MOD, RunModel_GR6J) & !identical(FUN_MOD, RunModel_CemaNeigeGR6J) &
+      #     !identical(FUN_MOD, RunModel_GR5H) & !identical(FUN_MOD, RunModel_CemaNeigeGR5H)) {
+      # if (is.null(IniStates)) {
+      #   IniResLevels <- as.double(c(0.3, 0.5, NA, NA))
+      # }
     }
   } else {
     if (!is.null(IniResLevels)) {
-      stop("IniResLevels can only be used with monthly or daily or hourly GR models \n")
+      stop("'IniResLevels' can only be used with monthly or daily or hourly GR models")
     }
   }
   ## check IniStates
-  if (is.null(IniStates) & is.null(IniResLevels) & verbose) {
-    warning("\t Model states initialisation not defined -> default configuration used \n")
+  if (is.null(IniStates) & is.null(IniResLevels) & warnings) {
+    warning("model states initialisation not defined: default configuration used")
   }
-  if (!is.null(IniStates) & !is.null(IniResLevels) & verbose) {
-    warning("\t IniStates and IniResLevels are both defined -> Store levels are taken from IniResLevels \n")
+  if (!is.null(IniStates) & !is.null(IniResLevels) & warnings) {
+    warning("'IniStates' and 'IniResLevels' are both defined: store levels are taken from 'IniResLevels'")
   }
   if ("CemaNeige" %in% ObjectClass) {
     NLayers <- length(InputsModel$LayerPrecip)
@@ -203,10 +226,10 @@ CreateRunOptions <- function(FUN_MOD, InputsModel, IndPeriod_WarmUp = NULL, IndP
   NState <- NULL
   if ("GR" %in% ObjectClass | "CemaNeige" %in% ObjectClass) {
     if ("hourly"  %in% ObjectClass) {
-      NState <- 7 + 3 * 24 * 20
+      NState <- 7 + 3 * 24 * 20 + 4 * NLayers
     }
     if ("daily"   %in% ObjectClass) {
-      NState <- 7 + 3 * 20 + 2 * NLayers
+      NState <- 7 + 3 * 20 + 4 * NLayers
     }
     if ("monthly" %in% ObjectClass) {
       NState <- 2
@@ -216,42 +239,58 @@ CreateRunOptions <- function(FUN_MOD, InputsModel, IndPeriod_WarmUp = NULL, IndP
     }
   }
   if (!is.null(IniStates)) {
-    
+
     if (!inherits(IniStates, "IniStates")) {
-      stop("IniStates must be an object of class IniStates\n")
-      return(NULL)
+      stop("'IniStates' must be an object of class 'IniStates'")
     }
     if (sum(ObjectClass %in% class(IniStates)) < 2) {
-      stop(paste0("Non convenient IniStates for this FUN_MOD\n"))
-      return(NULL)
+      stop(paste0("non convenient 'IniStates' for the chosen 'FUN_MOD'"))
     }
     if (identical(FUN_MOD, RunModel_GR1A) & !is.null(IniStates)) { ## GR1A
-      stop(paste0("IniStates is not available for this FUN_MOD\n"))
-      return(NULL)
+      stop(paste0("'IniStates' is not available for the chosen 'FUN_MOD'"))
     }
-    if ((identical(FUN_MOD, RunModel_GR5J) | identical(FUN_MOD, RunModel_CemaNeigeGR5J)) & !all(is.na(IniStates$UH$UH1))) { ## GR5J
-      stop(paste0("Non convenient IniStates for this FUN_MOD. In IniStates, UH1 has to be a vector of NA for GR5J \n"))
-      return(NULL)
+    if ((identical(FUN_MOD, RunModel_GR5J) | identical(FUN_MOD, RunModel_CemaNeigeGR5J) |
+         identical(FUN_MOD, RunModel_GR5H) | identical(FUN_MOD, RunModel_CemaNeigeGR5H)) &
+        !all(is.na(IniStates$UH$UH1))) { ## GR5J or GR5H
+      stop(paste0("non convenient 'IniStates' for the chosen 'FUN_MOD'.' In 'IniStates', 'UH1' has to be a vector of NA for GR5J"))
     }
     if ((identical(FUN_MOD, RunModel_GR6J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J)) & is.na(IniStates$Store$Exp)) { ## GR6J
-      stop(paste0("Non convenient IniStates for this FUN_MOD. GR6J needs an exponential store value in IniStates \n"))
-      return(NULL)
+      stop(paste0("non convenient 'IniStates' for the chosen 'FUN_MOD'.' GR6J needs an exponential store value in 'IniStates'"))
+    }
+    if ((identical(FUN_MOD, RunModel_GR5H) | identical(FUN_MOD, RunModel_CemaNeigeGR5H)) & is.na(IniStates$Store$Int)) { ## GR5H interception
+
+      stop(paste0("non convenient 'IniStates' for the chosen 'FUN_MOD'.' GR5H (with interception store) needs an interception store value in 'IniStates'"))
     }
     if (!(identical(FUN_MOD, RunModel_GR6J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J)) & !is.na(IniStates$Store$Exp)) { ## except GR6J
-      stop(paste0("Non convenient IniStates for this FUN_MOD. No exponential store value needed in IniStates \n"))
-      return(NULL)
+      stop(paste0("non convenient 'IniStates' for the chosen 'FUN_MOD'.' No exponential store value needed in 'IniStates'"))
+    }
+    if (!(identical(FUN_MOD, RunModel_GR5H) | identical(FUN_MOD, RunModel_CemaNeigeGR5H)) & !is.na(IniStates$Store$Int)) { ## except GR5H interception
+      stop(paste0("non convenient 'IniStates' for the chosen 'FUN_MOD'.' No interception store value needed in 'IniStates'"))
     }
     # if (length(na.omit(unlist(IniStates))) != NState) {
-    #   stop(paste0("The length of IniStates must be ", NState, " for the chosen FUN_MOD \n"))
-    #   return(NULL)
+    #   stop(paste0("the length of IniStates must be ", NState, " for the chosen FUN_MOD"))
     # }
+    if ((!"CemaNeige" %in% ObjectClass &  inherits(IniStates, "CemaNeige")) |
+        ( "CemaNeige" %in% ObjectClass & !inherits(IniStates, "CemaNeige"))) {
+      stop("'FUN_MOD' and 'IniStates' must be both of class 'CemaNeige'")
+    }
+    if (( "hysteresis" %in% ObjectClass & !inherits(IniStates, "hysteresis")) |
+        (!"hysteresis" %in% ObjectClass &  inherits(IniStates, "hysteresis"))) {
+      stop("'IsHyst' and 'IniStates' are not consistent on the use of the hysteresis")
+    }
     if (!"CemaNeige" %in% ObjectClass & any(is.na(IniStates$CemaNeigeLayers$G  ))) {
-      IniStates$CemaNeigeLayers$G   <- NULL
+      IniStates$CemaNeigeLayers$G <- NULL
     }
     if (!"CemaNeige" %in% ObjectClass & any(is.na(IniStates$CemaNeigeLayers$eTG))) {
       IniStates$CemaNeigeLayers$eTG <- NULL
     }
-    IniStates$Store$Rest <- rep(NA, 4)
+    if (!"CemaNeige" %in% ObjectClass & any(is.na(IniStates$CemaNeigeLayers$Gthr))) {
+      IniStates$CemaNeigeLayers$Gthr <- NULL
+    }
+    if (!"CemaNeige" %in% ObjectClass & any(is.na(IniStates$CemaNeigeLayers$Glocmax))) {
+      IniStates$CemaNeigeLayers$Glocmax <- NULL
+    }
+    IniStates$Store$Rest <- rep(NA, 3)
     IniStates <- unlist(IniStates)
     IniStates[is.na(IniStates)] <- 0
     if ("monthly" %in% ObjectClass) {
@@ -260,105 +299,69 @@ CreateRunOptions <- function(FUN_MOD, InputsModel, IndPeriod_WarmUp = NULL, IndP
   } else {
     IniStates <- as.double(rep(0.0, NState))
   }
-  
-  
+
+
   ##check_Outputs_Cal_and_Sim
-  
+
   ##Outputs_all
-  Outputs_all <- NULL
-  if (identical(FUN_MOD,RunModel_GR4H)) {
-    Outputs_all <- c(Outputs_all,"PotEvap","Precip","Prod","AE","Perc","PR","Q9","Q1","Rout","Exch","AExch","QR","QD","Qsim")
-  }
-  if (identical(FUN_MOD,RunModel_GR4J) | identical(FUN_MOD,RunModel_CemaNeigeGR4J)) {
-    Outputs_all <- c(Outputs_all,"PotEvap", "Precip", "Prod", "Pn", "Ps", "AE", "Perc", "PR", "Q9", "Q1", "Rout", "Exch",
-                     "AExch1", "AExch2", "AExch", "QR", "QD", "Qsim")
-  }
-  if (identical(FUN_MOD,RunModel_GR5J) | identical(FUN_MOD,RunModel_CemaNeigeGR5J)) {
-    Outputs_all <- c(Outputs_all,"PotEvap", "Precip", "Prod", "Pn", "Ps", "AE", "Perc", "PR", "Q9", "Q1", "Rout", "Exch",
-                     "AExch1", "AExch2", "AExch", "QR", "QD", "Qsim")
-  }
-  if (identical(FUN_MOD,RunModel_GR6J) | identical(FUN_MOD,RunModel_CemaNeigeGR6J)) {
-    Outputs_all <- c(Outputs_all,"PotEvap", "Precip", "Prod", "Pn", "Ps", "AE", "Perc", "PR", "Q9", "Q1", "Rout", "Exch",
-                     "AExch1", "AExch2", "AExch", "QR", "QRExp", "Exp", "QD", "Qsim")
-  }
-  if (identical(FUN_MOD,RunModel_GR2M)) {
-    Outputs_all <- c(Outputs_all,"PotEvap", "Precip", "AE", "Pn", "Perc", "PR", "Exch", "Prod", "Rout", "Qsim")
-  }
-  if (identical(FUN_MOD,RunModel_GR1A)) {
-    Outputs_all <- c(Outputs_all,"PotEvap","Precip","Qsim")
-  }
-  if ("CemaNeige" %in% ObjectClass) {
-    Outputs_all <- c(Outputs_all,"Pliq","Psol","SnowPack","ThermalState","Gratio","PotMelt","Melt","PliqAndMelt", "Temp")
+  Outputs_all <- c("DatesR", unlist(FortranOutputs), "WarmUpQsim", "StateEnd", "Param")
+  if (FeatFUN_MOD$IsSD) {
+    Outputs_all <- c(Outputs_all, "QsimDown", "Qsim_m3")
   }
-  
+
   ##check_Outputs_Sim
   if (!is.vector(Outputs_Sim)) {
-    stop("Outputs_Sim must be a vector of characters \n")
-    return(NULL)
+    stop("'Outputs_Sim' must be a vector of characters")
   }
   if (!is.character(Outputs_Sim)) {
-    stop("Outputs_Sim must be a vector of characters \n")
-    return(NULL)
+    stop("'Outputs_Sim' must be a vector of characters")
   }
   if (sum(is.na(Outputs_Sim)) != 0) {
-    stop("Outputs_Sim must not contain NA \n")
-    return(NULL)
+    stop("'Outputs_Sim' must not contain NA")
   }
   if ("all" %in% Outputs_Sim) {
-    Outputs_Sim <- c("DatesR", Outputs_all, "StateEnd")
+    Outputs_Sim <- Outputs_all
   }
-  Test <- which(Outputs_Sim %in% c("DatesR", Outputs_all, "StateEnd") == FALSE)
+  Test <- which(!Outputs_Sim %in% Outputs_all)
   if (length(Test) != 0) {
-    stop(paste0( "Outputs_Sim is incorrectly defined: ",
-                 paste(Outputs_Sim[Test], collapse = ", "), " not found \n"))
-    return(NULL)
-    
+    stop(paste0( "'Outputs_Sim' is incorrectly defined: ",
+                 paste(Outputs_Sim[Test], collapse = ", "), " not found"))
   }
   Outputs_Sim <- Outputs_Sim[!duplicated(Outputs_Sim)]
-  
-  
+
+
   ##check_Outputs_Cal
   if (is.null(Outputs_Cal)) {
     if ("GR" %in% ObjectClass) {
-      Outputs_Cal <- c("Qsim")
-    }
-    if ("CemaNeige" %in% ObjectClass) {
+      Outputs_Cal <- c("Qsim", "Param")
+      if ("CemaNeige" %in% ObjectClass) {
+        Outputs_Cal <- c("PliqAndMelt", Outputs_Cal)
+      }
+    } else if ("CemaNeige" %in% ObjectClass) {
       Outputs_Cal <- c("all")
     }
-    if ("GR" %in% ObjectClass &
-        "CemaNeige" %in% ObjectClass) {
-      Outputs_Cal <- c("PliqAndMelt", "Qsim")
-    }
   } else {
     if (!is.vector(Outputs_Cal)) {
-      stop("Outputs_Cal must be a vector of characters \n")
-      return(NULL)
+      stop("'Outputs_Cal' must be a vector of characters")
     }
     if (!is.character(Outputs_Cal)) {
-      stop("Outputs_Cal must be a vector of characters \n")
-      return(NULL)
+      stop("'Outputs_Cal' must be a vector of characters")
     }
     if (sum(is.na(Outputs_Cal)) != 0) {
-      stop("Outputs_Cal must not contain NA \n")
-      return(NULL)
+      stop("'Outputs_Cal' must not contain NA")
     }
   }
   if ("all" %in% Outputs_Cal) {
-    Outputs_Cal <- c("DatesR", Outputs_all, "StateEnd")
-    
+    Outputs_Cal <- Outputs_all
   }
-  Test <-
-    which(Outputs_Cal %in% c("DatesR", Outputs_all, "StateEnd") == FALSE)
+  Test <- which(!Outputs_Cal %in% Outputs_all)
   if (length(Test) != 0) {
-    stop(paste0("Outputs_Cal is incorrectly defined: ",
-                paste(Outputs_Cal[Test], collapse = ", "), " not found \n"))
-    return(NULL)
-    
-  }
-  Outputs_Cal <- Outputs_Cal[!duplicated(Outputs_Cal)]
-  
-  
-  
+    stop(paste0("'Outputs_Cal' is incorrectly defined: ",
+                paste(Outputs_Cal[Test], collapse = ", "), " not found"))
+  }
+  Outputs_Cal <- unique(Outputs_Cal)
+
+
   ##check_MeanAnSolidPrecip
   if ("CemaNeige" %in% ObjectClass & is.null(MeanAnSolidPrecip)) {
     NLayers <- length(InputsModel$LayerPrecip)
@@ -386,71 +389,94 @@ CreateRunOptions <- function(FUN_MOD, InputsModel, IndPeriod_WarmUp = NULL, IndP
       Factor <- 1
     }
     if (is.null(Factor)) {
-      stop("InputsModel must be of class 'hourly', 'daily', 'monthly' or 'yearly' \n")
-      return(NULL)
+      stop("'InputsModel' must be of class 'hourly', 'daily', 'monthly' or 'yearly'")
     }
     MeanAnSolidPrecip <- rep(mean(SolidPrecip) * Factor, NLayers)
     ### default value: same Gseuil for all layers
-    if (verbose) {
-      warning("\t MeanAnSolidPrecip not defined -> it was automatically set to c(",
-              paste(round(MeanAnSolidPrecip), collapse = ","), ") \n")
+    if (warnings) {
+      warning("'MeanAnSolidPrecip' not defined: it was automatically set to c(",
+              paste(round(MeanAnSolidPrecip), collapse = ","), ")  from the 'InputsModel' given to the function. ",
+              "Be careful in case your application is (short-term) forecasting.\n")
     }
   }
   if ("CemaNeige" %in% ObjectClass & !is.null(MeanAnSolidPrecip)) {
     if (!is.vector(MeanAnSolidPrecip)) {
-      stop(paste0("MeanAnSolidPrecip must be a vector of numeric values \n"))
-      return(NULL)
+      stop(paste0("'MeanAnSolidPrecip' must be a vector of numeric values"))
     }
     if (!is.numeric(MeanAnSolidPrecip)) {
-      stop(paste0("MeanAnSolidPrecip must be a vector of numeric values \n"))
-      return(NULL)
+      stop(paste0("'MeanAnSolidPrecip' must be a vector of numeric values"))
     }
     if (length(MeanAnSolidPrecip) != NLayers) {
-      stop(paste0("MeanAnSolidPrecip must be a numeric vector of length ", NLayers, " \n"))
-      return(NULL)
+      stop(paste0("'MeanAnSolidPrecip' must be a numeric vector of length ", NLayers, ""))
     }
   }
-  
-  
+
+
   ##check_PliqAndMelt
   if ("GR" %in% ObjectClass & "CemaNeige" %in% ObjectClass) {
-    if ("PliqAndMelt" %in% Outputs_Cal == FALSE & "all" %in% Outputs_Cal == FALSE) {
+    if (!"PliqAndMelt" %in% Outputs_Cal & !"all" %in% Outputs_Cal) {
       WTxt <- NULL
-      WTxt <- paste0(WTxt, "\t PliqAndMelt was not defined in Outputs_Cal but is needed to feed the hydrological model with the snow modele outputs \n")
-      WTxt <- paste0(WTxt, "\t -> it was automatically added \n")
-      if (!is.null(WTxt) & verbose) {
+      WTxt <- paste0(WTxt, "'PliqAndMelt' was not defined in 'Outputs_Cal' but is needed to feed the hydrological model with the snow modele outputs \n")
+      WTxt <- paste0(WTxt, ": it was automatically added \n")
+      if (!is.null(WTxt) & warnings) {
         warning(WTxt)
       }
       Outputs_Cal <- c(Outputs_Cal, "PliqAndMelt")
     }
-    if ("PliqAndMelt" %in% Outputs_Sim == FALSE & "all" %in% Outputs_Sim == FALSE) {
+    if (!"PliqAndMelt" %in% Outputs_Sim & !"all" %in% Outputs_Sim) {
       WTxt <- NULL
-      WTxt <- paste0(WTxt, "\t PliqAndMelt was not defined in Outputs_Sim but is needed to feed the hydrological model with the snow modele outputs \n")
-      WTxt <- paste0(WTxt, "\t -> it was automatically added \n")
-      if (!is.null(WTxt) & verbose) {
+      WTxt <- paste0(WTxt, "'PliqAndMelt' was not defined in 'Outputs_Sim' but is needed to feed the hydrological model with the snow modele outputs \n")
+      WTxt <- paste0(WTxt, ": it was automatically added \n")
+      if (!is.null(WTxt) & warnings) {
         warning(WTxt)
       }
       Outputs_Sim <- c(Outputs_Sim, "PliqAndMelt")
     }
   }
-  
-  
+
+
+  ##check_Qsim
+  if ("GR" %in% ObjectClass) {
+    if (!"Qsim" %in% Outputs_Cal & !"all" %in% Outputs_Cal) {
+      WTxt <- NULL
+      WTxt <- paste0(WTxt, "'Qsim' was not defined in 'Outputs_Cal' \n")
+      WTxt <- paste0(WTxt, ": it was automatically added \n")
+      if (!is.null(WTxt) & warnings) {
+        warning(WTxt)
+      }
+      Outputs_Cal <- c(Outputs_Cal, "Qsim")
+    }
+    if (!"Qsim" %in% Outputs_Sim & !"all" %in% Outputs_Sim) {
+      WTxt <- NULL
+      WTxt <- paste0(WTxt, "'Qsim' was not defined in 'Outputs_Sim' \n")
+      WTxt <- paste0(WTxt, ": it was automatically added \n")
+      if (!is.null(WTxt) & warnings) {
+        warning(WTxt)
+      }
+      Outputs_Sim <- c(Outputs_Sim, "Qsim")
+    }
+  }
+
   ##Create_RunOptions
   RunOptions <- list(IndPeriod_WarmUp = IndPeriod_WarmUp,
                      IndPeriod_Run = IndPeriod_Run,
                      IniStates = IniStates,
                      IniResLevels = IniResLevels,
                      Outputs_Cal = Outputs_Cal,
-                     Outputs_Sim = Outputs_Sim)
-  
+                     Outputs_Sim = Outputs_Sim,
+                     FortranOutputs = FortranOutputs,
+                     FeatFUN_MOD = FeatFUN_MOD)
+
   if ("CemaNeige" %in% ObjectClass) {
-    RunOptions <-
-      c(RunOptions, list(MeanAnSolidPrecip = MeanAnSolidPrecip))
+    RunOptions <- c(RunOptions, list(MeanAnSolidPrecip = MeanAnSolidPrecip))
+  }
+  if ("interception" %in% ObjectClass) {
+    RunOptions <- c(RunOptions, list(Imax = Imax))
   }
   class(RunOptions) <- c("RunOptions", ObjectClass)
-  
+
   return(RunOptions)
-  
-  
+
+
 }