diff --git a/.Rbuildignore b/.Rbuildignore
index 7c1c5baa8f03668a04b8d352020ed07372de4599..acd9e68a9a2e50eff8ef783a77b63bab66e63424 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -8,3 +8,4 @@
^\.gitlab-ci\.yml$
^\.vscode$
^Rplots\.pdf$
+^ci$
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 73d31f89ad7f752944b114e78ad61f76eab5b84a..5019ac1352059b7b2b59b477057deee4cc35084f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,36 +1,14 @@
stages:
- - update_packages
- - build
+ - check
- regression
- - tests
+ - revdepcheck
default:
before_script:
- echo "setwd(\"$(pwd)\")" > .Rprofile
+ - echo ".libPaths <- c(Sys.getenv(\"R_LIBS_USER\"), .libPaths())" >> .Rprofile
- PATH=~/R/sources/R-${R_VERSION}/bin:$PATH
- - rename "s/${R_VERSION}.airGR/airGR/" *.tar.gz
- - R -e 'chooseCRANmirror(graphics = FALSE, ind = 1); pkg <- "caRamel"; pkgInst <- installed.packages()[, "Package"]; pkgMiss <- setdiff(pkg, pkgInst); if (length(pkgMiss) > 0) install.packages(pkgMiss)'
-
-.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
+ - R -e 'remotes::install_deps(dep = T)'
.regression:
stage: regression
@@ -40,27 +18,20 @@ default:
- Rscript tests/testthat/regression_tests.R dev
- Rscript tests/testthat/regression_tests.R compare
+.check:
+ stage: check
+ script:
+ - R -e ' rcmdcheck::rcmdcheck(args = ifelse(as.logical(Sys.getenv("NOT_CRAN")), "", "--as-cran"), error_on = "warning")'
+
.check_not_cran:
- stage: tests
variables:
NOT_CRAN: "true"
- script:
- - R CMD check airGR_*.tar.gz
+ extends: .check
.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
+ NOT_CRAN: "false"
+ extends: .check
regression_patched:
variables:
@@ -93,20 +64,6 @@ check_as_cran_patched:
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:
@@ -125,35 +82,39 @@ check_as_cran_devel:
R_VERSION: "devel"
extends: .check_as_cran
-update_packages_oldrel:
- variables:
- R_VERSION: "oldrel"
- extends: .update_packages
-
-build_oldrel:
+check_not_cran_oldrel:
only:
refs:
- tags
- schedules
variables:
R_VERSION: "oldrel"
- extends: .build
+ extends: .check_not_cran
-check_not_cran_oldrel:
+check_as_cran_oldrel:
only:
refs:
- tags
- schedules
variables:
R_VERSION: "oldrel"
- extends: .check_not_cran
+ extends: .check_as_cran
-check_as_cran_oldrel:
+revdepcheck_patched:
+ stage: revdepcheck
only:
refs:
- tags
- schedules
variables:
- R_VERSION: "oldrel"
- extends: .check_as_cran
-
+ R_VERSION: "patched"
+ script:
+ - R -e 'remotes::install_github("https://github.com/r-lib/revdepcheck")'
+ - R -e 'revdepcheck::revdep_check(num_workers = 2)'
+ - R -e 'if (any(sapply(revdepcheck::revdep_summary(), function(x) {any(x$cmp$change == 1)}))) stop()'
+ artifacts:
+ paths:
+ - revdep/README.md
+ - revdep/problems.md
+ - revdep/failures.md
+ - revdep/cran.md
diff --git a/R/Calibration.R b/R/Calibration.R
index 2bfceaf482145a80b51a80953787323c133f1c3c..a66c78154e42b49ab80a61db832a6327da4dd962 100644
--- a/R/Calibration.R
+++ b/R/Calibration.R
@@ -1,13 +1,14 @@
-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, ...))
}
diff --git a/man/Calibration.Rd b/man/Calibration.Rd
index c4779f0bd4ffa5478cdaaf36a3fc4a1783e5a04a..7368556f2202b4d24ecfbc9badb85d888fd3fd3c 100644
--- a/man/Calibration.Rd
+++ b/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}}.
}