Resolve "Gitlab-CI: correctly handle WARNING and NOTE in checks"

Closes #86 (closed)

R/Calibration.R

-Calibration <- function(InputsModel, 
-                        RunOptions, 
-                        InputsCrit, 
+Calibration <- function(InputsModel,
+                        RunOptions,
+                        InputsCrit,
                         CalibOptions,
-                        FUN_MOD, 
+                        FUN_MOD,
                         FUN_CRIT,                      # deprecated
-                        FUN_CALIB = Calibration_Michel, 
+                        FUN_CALIB = Calibration_Michel,
                         FUN_TRANSFO = NULL,
-                        verbose = TRUE) {
-  
+                        verbose = TRUE,
+                        ...) {
+
   FUN_MOD   <- match.fun(FUN_MOD)
   if (!missing(FUN_CRIT)) {
     FUN_CRIT <- match.fun(FUN_CRIT)
@@ -16,10 +17,10 @@ Calibration <- function(InputsModel,
   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))
+                   verbose = verbose, ...))
 }
 

man/Calibration.Rd

@@ -16,7 +16,7 @@ Calibration algorithm that optimises the error criterion selected as objective f
 \usage{
 Calibration(InputsModel, RunOptions, InputsCrit, CalibOptions,
             FUN_MOD, FUN_CRIT, FUN_CALIB = Calibration_Michel,
-            FUN_TRANSFO = NULL, verbose = TRUE)
+            FUN_TRANSFO = NULL, verbose = TRUE, ...)
 }
 
 
@@ -38,6 +38,8 @@ Calibration(InputsModel, RunOptions, InputsCrit, CalibOptions,
 \item{FUN_TRANSFO}{(optional) [function] model parameters transformation function, if the \code{FUN_MOD} used is native in the package \code{FUN_TRANSFO} is automatically defined}
 
 \item{verbose}{(optional) [boolean] boolean indicating if the function is run in verbose mode or not, default = \code{TRUE}}
+
+\item{...}{Further arguments to pass to \code{\link{RunModel}}}
 }
 
 
@@ -53,11 +55,11 @@ library(airGR)
 data(L0123001)
 
 ## preparation of InputsModel object
-InputsModel <- CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR, 
+InputsModel <- CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR,
                                  Precip = BasinObs$P, PotEvap = BasinObs$E)
 
 ## calibration period selection
-Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"), 
+Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
                which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
 
 ## preparation of RunOptions object
@@ -65,7 +67,7 @@ RunOptions <- CreateRunOptions(FUN_MOD = RunModel_GR4J,
                                InputsModel = InputsModel, IndPeriod_Run = Ind_Run)
 
 ## calibration criterion: preparation of the InputsCrit object
-InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel, 
+InputsCrit <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel,
                                RunOptions = RunOptions, Obs = BasinObs$Qmm[Ind_Run])
 
 ## preparation of CalibOptions object
@@ -74,24 +76,24 @@ CalibOptions <- CreateCalibOptions(FUN_MOD = RunModel_GR4J, FUN_CALIB = Calibrat
 ## calibration
 OutputsCalib <- Calibration(InputsModel = InputsModel, RunOptions = RunOptions,
                             InputsCrit = InputsCrit, CalibOptions = CalibOptions,
-                            FUN_MOD = RunModel_GR4J, 
+                            FUN_MOD = RunModel_GR4J,
                             FUN_CALIB = Calibration_Michel)
 
 ## simulation
 Param <- OutputsCalib$ParamFinalR
-OutputsModel <- RunModel(InputsModel = InputsModel, RunOptions = RunOptions, 
+OutputsModel <- RunModel(InputsModel = InputsModel, RunOptions = RunOptions,
                          Param = Param, FUN = RunModel_GR4J)
 
 ## results preview
 plot(OutputsModel, Qobs = BasinObs$Qmm[Ind_Run])
 
 ## efficiency criterion: Nash-Sutcliffe Efficiency
-InputsCrit  <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel, 
+InputsCrit  <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModel,
                                 RunOptions = RunOptions, Obs = BasinObs$Qmm[Ind_Run])
 OutputsCrit <- ErrorCrit_NSE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
 
 ## efficiency criterion: Kling-Gupta Efficiency
-InputsCrit  <- CreateInputsCrit(FUN_CRIT = ErrorCrit_KGE, InputsModel = InputsModel, 
+InputsCrit  <- CreateInputsCrit(FUN_CRIT = ErrorCrit_KGE, InputsModel = InputsModel,
                                 RunOptions = RunOptions, Obs = BasinObs$Qmm[Ind_Run])
 OutputsCrit <- ErrorCrit_KGE(InputsCrit = InputsCrit, OutputsModel = OutputsModel)
 }
@@ -105,7 +107,7 @@ Laurent Coron, Olivier Delaigue
 \seealso{
 \code{\link{Calibration_Michel}},
 \code{\link{ErrorCrit}}, \code{\link{TransfoParam}},
-\code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}}, 
+\code{\link{CreateInputsModel}}, \code{\link{CreateRunOptions}},
 \code{\link{CreateInputsCrit}}, \code{\link{CreateCalibOptions}}.
 }
 

man/Calibration_Michel.Rd

@@ -19,7 +19,7 @@ Then a steepest descent local search algorithm is performed, starting from the r
 
 \usage{
 Calibration_Michel(InputsModel, RunOptions, InputsCrit, CalibOptions,
-                   FUN_MOD, FUN_CRIT, FUN_TRANSFO = NULL, verbose = TRUE)
+                   FUN_MOD, FUN_CRIT, FUN_TRANSFO = NULL, verbose = TRUE, ...)
 }
 
 
@@ -39,6 +39,8 @@ Calibration_Michel(InputsModel, RunOptions, InputsCrit, CalibOptions,
 \item{FUN_TRANSFO}{(optional) [function] model parameters transformation function, if the \code{FUN_MOD} used is native in the package \code{FUN_TRANSFO} is automatically defined}
 
 \item{verbose}{(optional) [boolean] boolean indicating if the function is run in verbose mode or not, default = \code{TRUE}}
+
+\item{...}{Further arguments to pass to \code{\link{RunModel}}}
 }
 
 

man/RunModel.Rd

@@ -15,7 +15,7 @@ Function which performs a single model run with the provided function over the s
 
 
 \usage{
-RunModel(InputsModel, RunOptions, Param, FUN_MOD)
+RunModel(InputsModel, RunOptions, Param, FUN_MOD, ...)
 %
 %\method{[}{OutputsModel}(x, i)
 }
@@ -33,6 +33,7 @@ RunModel(InputsModel, RunOptions, Param, FUN_MOD)
 %\item{x}{[InputsModel] object of class InputsModel}
 %
 %\item{i}{[integer] of the indices to subset a time series or [character] names of the elements to extract}
+\item{...}{Further arguments to pass to the hydrological model function. See \code{\link{RunModel_Lag}} for example}
 }
 
 

.gitlab-ci.yml

@@ -20,7 +20,7 @@ default:
     - cd ..
     - echo "setwd(\"$(pwd)\")" > .Rprofile
     - R -e 'utils::install.packages("usethis", repo = "https://cloud.r-project.org/")'
-    - R -e 'remotes::install_deps(dep = T)'
+    - R -e 'remotes::install_deps(pkgdir = "airgr", dep = T)'
     - R CMD build airgr
     - rename "s/airGR/${R_VERSION}.airGR/" airGR_*.tar.gz
     - mv *.tar.gz airgr/