Merge branch 'dev' into 'master'

CRAN v1.6.9.21

See merge request HYCAR-Hydro/airgr!26

.Rbuildignore

@@ -2,3 +2,9 @@
 ^\.Rproj\.user$
 ^\.Rprofile$
 ^packrat/
+^tests/tmp/
+^\.gitlab-ci.yml$
+^\.regressionignore$
+^\.gitlab-ci\.yml$
+^\.vscode$
+^Rplots\.pdf$

.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
+
+
+######################################################################################################
+### 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
+
+# pkgdown site
+docs/
+
+# vscode IDE
+.vscode/*
+*.code-workspace
+.history/

.gitlab-ci.yml

+stages:
+  - update_packages
+  - build
+  - regression
+  - tests
+
+default:
+  before_script:
+    - echo "setwd(\"$(pwd)\")" > .Rprofile
+    - PATH=~/R/sources/R-${R_VERSION}/bin:$PATH
+    - rename "s/${R_VERSION}.airGR/airGR/" *.tar.gz
+
+.update_packages:
+  stage: update_packages
+  only:
+    refs:
+      - tags
+      - schedules
+  script:
+    - Rscript -e "update.packages(ask=FALSE, repos=\"http://cran.r-project.org\")"
+
+.build:
+  stage: build
+  script:
+    - cd ..
+    - echo "setwd(\"$(pwd)\")" > .Rprofile
+    - R CMD build airgr
+    - rename "s/airGR/${R_VERSION}.airGR/" airGR_*.tar.gz
+    - mv *.tar.gz airgr/
+  artifacts:
+    untracked: true
+    expire_in: 1 week
+
+.regression:
+  stage: regression
+  script:
+    - Rscript tests/testthat/regression_tests.R stable
+    - R CMD INSTALL .
+    - Rscript tests/testthat/regression_tests.R dev
+    - Rscript tests/testthat/regression_tests.R compare
+
+.check_not_cran:
+  stage: tests
+  variables:
+    NOT_CRAN: "true"
+  script:
+    - R CMD check airGR_*.tar.gz
+
+.check_as_cran:
+  stage: tests
+  script:
+    - R CMD check --as-cran airGR_*.tar.gz
+
+update_packages_patched:
+  variables:
+    R_VERSION: "patched"
+  extends: .update_packages
+
+build_patched:
+  variables:
+    R_VERSION: "patched"
+  extends: .build
+
+regression_patched:
+  variables:
+    R_VERSION: "patched"
+  extends: .regression
+
+regression_devel:
+  only:
+    refs:
+      - schedules
+  variables:
+    R_VERSION: "devel"
+  extends: .regression
+
+regression_oldrel:
+  only:
+    refs:
+      - schedules
+  variables:
+    R_VERSION: "oldrel"
+  extends: .regression
+
+check_not_cran_patched:
+  variables:
+    R_VERSION: "patched"
+  extends: .check_not_cran
+
+check_as_cran_patched:
+  variables:
+    R_VERSION: "patched"
+  extends: .check_as_cran
+
+update_packages_devel:
+  variables:
+    R_VERSION: "devel"
+  extends: .update_packages
+
+build_devel:
+  only:
+    refs:
+      - tags
+      - schedules
+  variables:
+    R_VERSION: "devel"
+  extends: .build
+
+check_not_cran_devel:
+  only:
+    refs:
+      - tags
+      - schedules
+  variables:
+    R_VERSION: "devel"
+  extends: .check_not_cran
+
+check_as_cran_devel:
+  only:
+    refs:
+      - tags
+      - schedules
+  variables:
+    R_VERSION: "devel"
+  extends: .check_as_cran
+
+update_packages_oldrel:
+  variables:
+    R_VERSION: "oldrel"
+  extends: .update_packages
+
+build_oldrel:
+  only:
+    refs:
+      - tags
+      - schedules
+  variables:
+    R_VERSION: "oldrel"
+  extends: .build
+
+check_not_cran_oldrel:
+  only:
+    refs:
+      - tags
+      - schedules
+  variables:
+    R_VERSION: "oldrel"
+  extends: .check_not_cran
+
+check_as_cran_oldrel:
+  only:
+    refs:
+      - tags
+      - schedules
+  variables:
+    R_VERSION: "oldrel"
+  extends: .check_as_cran
+

.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].
+# Example for ignoring OutputsModel variable produced by example("RunModel_GR2M"): RunModel_GR2M OutputsModel
+RunModel_GR1A BasinObs
+RunModel_GR1A ConvertFun
+RunModel_GR1A NewTabSeries
+RunModel_GR1A NewTimeFormat
+RunModel_GR1A OutputsModel
+RunModel_GR1A TabSeries
+RunModel_GR1A TimeFormat
+RunModel_GR1A YearFirstMonth
+RunModel_GR2M BasinObs
+RunModel_GR2M ConvertFun
+RunModel_GR2M NewTabSeries
+RunModel_GR2M NewTimeFormat
+RunModel_GR2M OutputsModel
+RunModel_GR2M RunOptions
+RunModel_GR1A OutputsModel
+Calibration_Michel CalibOptions
+Calibration CalibOptions
+CreateCalibOptions CalibOptions
+
+# New version of the SeriesAggreg function
+RunModel_GR2M TabSeries
+RunModel_GR2M TimeFormat
+SeriesAggreg BasinInfo
+SeriesAggreg BasinObs
+SeriesAggreg NewTabSeries

DESCRIPTION

 Package: airGR
 Type: Package
 Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling
-Version: 1.4.3.65
-Date: 2020-02-28
+Version: 1.6.9.21
+Date: 2021-01-13
 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"), comment = c(ORCID = "0000-0002-1444-1830")),
+  person("David", "Dorchies", role = c("aut"), comment = c(ORCID = "0000-0002-6595-7984")),
   person("Charles", "Perrin", role = c("aut", "ths"), comment = c(ORCID = "0000-0001-8552-1881")),
   person("Claude", "Michel", role = c("aut", "ths")),
   person("Vazken", "Andréassian", role = c("ctb", "ths"), 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"), comment = c(ORCID = "0000-0002-4142-4454")),
@@ -19,12 +20,20 @@ Authors@R: c(
   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, Rmalschains
+Depends: R (>= 3.1.0)
+Imports:
+  graphics,
+  grDevices,
+  stats,
+  utils
+Suggests:
+  knitr, rmarkdown,
+  coda, DEoptim, dplyr, FME, ggmcmc, hydroPSO, imputeTS, Rmalschains,
+  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), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
 License: GPL-2
 URL: https://hydrogr.github.io/airGR/
-BugReports: https://gitlab.irstea.fr/HYCAR-Hydro/airgr/issues
+BugReports: https://gitlab.irstea.fr/HYCAR-Hydro/airgr/-/issues
 NeedsCompilation: yes
 Encoding: UTF-8
 VignetteBuilder: knitr

NAMESPACE

@@ -8,7 +8,13 @@ useDynLib(airGR, .registration = TRUE)
 #####################################
 ##            S3 methods           ##
 #####################################
-S3method("plot", "OutputsModel")
+S3method('[', InputsModel)
+S3method('[', OutputsModel)
+S3method(plot, OutputsModel)
+S3method(SeriesAggreg, data.frame)
+S3method(SeriesAggreg, list)
+S3method(SeriesAggreg, InputsModel)
+S3method(SeriesAggreg, OutputsModel)
 
 
 
@@ -45,6 +51,7 @@ export(RunModel_GR5H)
 export(RunModel_GR4J)
 export(RunModel_GR5J)
 export(RunModel_GR6J)
+export(RunModel_Lag)
 export(SeriesAggreg)
 export(TransfoParam)
 export(TransfoParam_CemaNeige)
@@ -56,10 +63,8 @@ export(TransfoParam_GR5H)
 export(TransfoParam_GR4J)
 export(TransfoParam_GR5J)
 export(TransfoParam_GR6J)
-export(plot.OutputsModel)
-exportPattern(".FortranOutputs")
-exportPattern(".ErrorCrit")
-
+export(TransfoParam_Lag)
+export(.ErrorCrit)
 
 
 #####################################

R/Calibration_Michel.R

-Calibration_Michel <- function(InputsModel, 
-                               RunOptions, 
-                               InputsCrit, 
+Calibration_Michel <- function(InputsModel,
+                               RunOptions,
+                               InputsCrit,
                                CalibOptions,
-                               FUN_MOD, 
+                               FUN_MOD,
                                FUN_CRIT,           # deprecated
-                               FUN_TRANSFO = NULL, 
+                               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'")
-  }  
+  }
   if (!inherits(RunOptions, "RunOptions")) {
     stop("'RunOptions' must be of class 'RunOptions'")
-  }  
+  }
   if (!inherits(InputsCrit, "InputsCrit")) {
     stop("'InputsCrit' must be of class 'InputsCrit'")
   }
@@ -46,106 +51,15 @@ Calibration_Michel <- function(InputsModel,
   }
   if (!inherits(CalibOptions, "CalibOptions")) {
     stop("'CalibOptions' must be of class 'CalibOptions'")
-  }  
+  }
   if (!inherits(CalibOptions, "HBAN")) {
     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")
-  }  
-  
-  
-  ##_check_FUN_TRANSFO
-  if (is.null(FUN_TRANSFO)) {
-    if (identical(FUN_MOD, RunModel_GR4H         )) {
-      FUN_TRANSFO <- TransfoParam_GR4H
-    }
-    if (identical(FUN_MOD, RunModel_GR5H         )) {
-      FUN_TRANSFO <- TransfoParam_GR5H
-    }
-    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    )) {
-      if (inherits(CalibOptions, "hysteresis")) {
-        FUN_TRANSFO <- TransfoParam_CemaNeigeHyst
-      } else {
-        FUN_TRANSFO <- TransfoParam_CemaNeige
-      }
-    }
-    if (identical(FUN_MOD, RunModel_CemaNeigeGR4H) | identical(FUN_MOD, RunModel_CemaNeigeGR5H) |
-        identical(FUN_MOD, RunModel_CemaNeigeGR4J) | identical(FUN_MOD, RunModel_CemaNeigeGR5J) | identical(FUN_MOD, RunModel_CemaNeigeGR6J)) {
-      if (identical(FUN_MOD, RunModel_CemaNeigeGR4H)) {
-        FUN1 <- TransfoParam_GR4H
-      }
-      if (identical(FUN_MOD, RunModel_CemaNeigeGR5H)) {
-        FUN1 <- TransfoParam_GR5H
-      }
-      if (identical(FUN_MOD, RunModel_CemaNeigeGR4J)) {
-        FUN1 <- TransfoParam_GR4J
-      }
-      if (identical(FUN_MOD, RunModel_CemaNeigeGR5J)) {
-        FUN1 <- TransfoParam_GR5J
-      }
-      if (identical(FUN_MOD, RunModel_CemaNeigeGR6J)) {
-        FUN1 <- TransfoParam_GR6J
-      }
-      if (inherits(CalibOptions, "hysteresis")) {
-        FUN2 <- TransfoParam_CemaNeigeHyst
-      } else {
-        FUN2 <- TransfoParam_CemaNeige
-      }
-      if (inherits(CalibOptions, "hysteresis")) {
-        FUN_TRANSFO <- function(ParamIn, Direction) {
-          Bool <- is.matrix(ParamIn)
-          if (!Bool) {
-            ParamIn <- rbind(ParamIn)
-          }
-          ParamOut <- NA * ParamIn
-          NParam   <- ncol(ParamIn)
-          ParamOut[,          1:(NParam-4)] <- FUN1(ParamIn[,          1:(NParam-4)], Direction)
-          ParamOut[, (NParam-3):NParam    ] <- FUN2(ParamIn[, (NParam-3):NParam    ], Direction)
-          if (!Bool) {
-            ParamOut <- ParamOut[1, ]
-          }
-          return(ParamOut)
-        }
-      } else {
-        FUN_TRANSFO <- function(ParamIn, Direction) {
-          Bool <- is.matrix(ParamIn)
-          if (!Bool) {
-            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) {
-            ParamOut <- ParamOut[1, ]
-          }
-          return(ParamOut)
-        }
-      }
-      
-    }
-    if (is.null(FUN_TRANSFO)) {
-      stop("'FUN_TRANSFO' was not found (in 'Calibration' function)")
-    }
   }
-  
-  ##_variables_initialisation 
+
+  ##_variables_initialisation
   ParamFinalR <- NULL
   ParamFinalT <- NULL
   CritFinal   <- NULL
@@ -174,20 +88,20 @@ Calibration_Michel <- function(InputsModel,
   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
   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)
-  }    
-  
-  
+  }
+
+
   ##Creation_of_new_candidates_______________________________________________
   OptimParam <- is.na(CalibOptions$FixedParam)
   if (PrefilteringType == 1) {
@@ -208,7 +122,7 @@ Calibration_Michel <- function(InputsModel,
   } else {
     CandidatesParamR <- cbind(CandidatesParamR)
   }
-  
+
   ##Loop_to_test_the_various_candidates______________________________________
   iNewOptim <- 0
   Ncandidates <- nrow(CandidatesParamR)
@@ -227,12 +141,12 @@ Calibration_Michel <- function(InputsModel,
         if (iNew == round(k / 10 * Ncandidates)) {
           message(" ", 10 * k, "%", appendLF = FALSE)
         }
-      } 
+      }
     }
     ##Model_run
     Param <- CandidatesParamR[iNew, ]
-    OutputsModel <- FUN_MOD(InputsModel, RunOptions, Param)
-    
+    OutputsModel <- RunModel(InputsModel, RunOptions, Param, FUN_MOD = FUN_MOD)
+
     ##Calibration_criterion_computation
     OutputsCrit <- ErrorCrit(InputsCrit, OutputsModel, verbose = FALSE)
     if (!is.na(OutputsCrit$CritValue)) {
@@ -251,8 +165,8 @@ Calibration_Michel <- function(InputsModel,
   if (verbose & Ncandidates > 1) {
     message(" 100%)\n", appendLF = FALSE)
   }
-  
-  
+
+
   ##End_of_first_step_Parameter_Screening____________________________________
   ParamStartR <- CandidatesParamR[iNewOptim, ]
   if (!is.matrix(ParamStartR)) {
@@ -275,13 +189,13 @@ Calibration_Michel <- function(InputsModel,
   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) {
     ##Format_checking
@@ -332,11 +246,11 @@ Calibration_Michel <- function(InputsModel,
     Output$NewCandidatesT <- matrix(VECT, ncol = NParam, byrow = TRUE)
     return(Output)
   }
-  
-  
+
+
   ##Initialisation_of_variables
   if (verbose) {
-    message("Steepest-descent local search in progress") 
+    message("Steepest-descent local search in progress")
   }
   Pace <- 0.64
   PaceDiag <- rep(0, NParam)
@@ -348,18 +262,18 @@ Calibration_Michel <- function(InputsModel,
   RangesT <- FUN_TRANSFO(RangesR, "RT")
   NewParamOptimT <- ParamStartT
   OldParamOptimT <- ParamStartT
-  
-  
+
+
   ##START_LOOP_ITER_________________________________________________________
   for (ITER in 1:(100 * NParam)) {
-    
-    
+
+
     ##Exit_loop_when_Pace_becomes_too_small___________________________________
     if (Pace < 0.01) {
       break
     }
-    
-    
+
+
     ##Creation_of_new_candidates______________________________________________
     CandidatesParamT <- ProposeCandidatesLoc(NewParamOptimT, OldParamOptimT, RangesT, OptimParam, Pace)$NewCandidatesT
     CandidatesParamR <- FUN_TRANSFO(CandidatesParamT, "TR")
@@ -373,16 +287,16 @@ Calibration_Michel <- function(InputsModel,
     } else {
       CandidatesParamR <- cbind(CandidatesParamR)
     }