From 4ce6ecc73bf961ddf04b2816699b270d5d97b5c0 Mon Sep 17 00:00:00 2001
From: Delaigue Olivier <olivier.delaigue@irstea.fr>
Date: Fri, 29 Jan 2021 02:56:08 +0100
Subject: [PATCH] v1.6.10.3 docs(vignette): add line breaks to avoid too long
 code lines in sd_model vignette

---
 DESCRIPTION                |  6 ++--
 NEWS.md                    |  2 +-
 vignettes/V05_sd_model.Rmd | 64 ++++++++++++++++++++++++--------------
 3 files changed, 45 insertions(+), 27 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 11139a61..b6d315ca 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: airGR
 Type: Package
 Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling
-Version: 1.6.10.2
-Date: 2021-01-28
+Version: 1.6.10.3
+Date: 2021-01-29
 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"),
@@ -29,7 +29,7 @@ Imports:
 Suggests:
   knitr, rmarkdown,
   caRamel, coda, DEoptim, dplyr, FME, ggmcmc, hydroPSO, imputeTS, Rmalschains,
-  ggplot2, GGally,
+  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), 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
diff --git a/NEWS.md b/NEWS.md
index 4743cdc6..b87f6aa6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,7 +2,7 @@
 
 
 
-### 1.6.10.2 Release Notes (2021-01-28)
+### 1.6.10.3 Release Notes (2021-01-29)
 
 #### New features
 
diff --git a/vignettes/V05_sd_model.Rmd b/vignettes/V05_sd_model.Rmd
index 5e814abc..265fe8a0 100644
--- a/vignettes/V05_sd_model.Rmd
+++ b/vignettes/V05_sd_model.Rmd
@@ -69,10 +69,12 @@ InputsModelUp <- CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$Da
 Ind_Run <- seq(which(format(BasinObs$DatesR, format = "%Y-%m-%d") == "1990-01-01"),
                which(format(BasinObs$DatesR, format = "%Y-%m-%d") == "1999-12-31"))
 RunOptionsUp <- CreateRunOptions(FUN_MOD = RunModel_GR4J,
-                                 InputsModel = InputsModelUp, IndPeriod_Run = Ind_Run,
-                                 IniStates = NULL, IniResLevels = NULL, IndPeriod_WarmUp = NULL)
+                                 InputsModel = InputsModelUp
+                                 , IndPeriod_WarmUp = NULL, IndPeriod_Run = Ind_Run,
+                                 IniStates = NULL, IniResLevels = NULL)
 InputsCritUp <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModelUp,
-                                 RunOptions = RunOptionsUp, VarObs = "Q", Obs = BasinObs$Qmm[Ind_Run])
+                                 RunOptions = RunOptionsUp,
+                                 VarObs = "Q", Obs = BasinObs$Qmm[Ind_Run])
 CalibOptionsUp <- CreateCalibOptions(FUN_MOD = RunModel_GR4J, FUN_CALIB = Calibration_Michel)
 OutputsCalibUp <- Calibration_Michel(InputsModel = InputsModelUp, RunOptions = RunOptionsUp,
                                      InputsCrit = InputsCritUp, CalibOptions = CalibOptionsUp,
@@ -101,9 +103,9 @@ we need to create the `InputsModel` object completed with upstream information:
 InputsModelDown1 <- CreateInputsModel(
   FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR,
   Precip = BasinObs$P, PotEvap = BasinObs$E,
-  Qupstream = matrix(QObsUp, ncol = 1), # Upstream observed flow
-  LengthHydro = 100 * 1000, # Distance between upstream catchment outlet and the downstream one in m
-  BasinAreas = c(180, 180) # Upstream and downstream areas in km²
+  Qupstream = matrix(QObsUp, ncol = 1), # upstream observed flow
+  LengthHydro = 1e2 * 1e3, # distance between upstream catchment outlet & the downstream one [m]
+  BasinAreas = c(180, 180) # upstream and downstream areas [km²]
 )
 ```
 
@@ -111,15 +113,19 @@ And then calibrate the combination of Lag model for upstream flow transfer and G
 
 ```{r}
 RunOptionsDown <- CreateRunOptions(FUN_MOD = RunModel_GR4J,
-                                   InputsModel = InputsModelDown1, IndPeriod_Run = Ind_Run,
-                                   IniStates = NULL, IniResLevels = NULL, IndPeriod_WarmUp = NULL)
+                                   InputsModel = InputsModelDown1,
+                                   IndPeriod_WarmUp = NULL, IndPeriod_Run = Ind_Run,
+                                   IniStates = NULL, IniResLevels = NULL)
 InputsCritDown <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE, InputsModel = InputsModelDown1,
-                                   RunOptions = RunOptionsDown, VarObs = "Q", Obs = QObsDown[Ind_Run])
+                                   RunOptions = RunOptionsDown,
+                                   VarObs = "Q", Obs = QObsDown[Ind_Run])
 CalibOptionsDown <- CreateCalibOptions(FUN_MOD = RunModel_GR4J,
                                        FUN_CALIB = Calibration_Michel,
-                                       IsSD = TRUE) # Don't forget to specify that it's an SD model here
-OutputsCalibDown1 <- Calibration_Michel(InputsModel = InputsModelDown1, RunOptions = RunOptionsDown,
-                                        InputsCrit = InputsCritDown, CalibOptions = CalibOptionsDown,
+                                       IsSD = TRUE) # specify that it's a SD model
+OutputsCalibDown1 <- Calibration_Michel(InputsModel = InputsModelDown1,
+                                        RunOptions = RunOptionsDown,
+                                        InputsCrit = InputsCritDown,
+                                        CalibOptions = CalibOptionsDown,
                                         FUN_MOD = RunModel_GR4J)
 ```
 
@@ -151,8 +157,10 @@ CritDown1 <- ErrorCrit_NSE(InputsCritDown, OutputsModelDown1)
 We calibrate the model with the `InputsModel` object previously created for substituting the observed upstream flow with the simulated one:
 
 ```{r}
-OutputsCalibDown2 <- Calibration_Michel(InputsModel = InputsModelDown2, RunOptions = RunOptionsDown,
-                                        InputsCrit = InputsCritDown, CalibOptions = CalibOptionsDown,
+OutputsCalibDown2 <- Calibration_Michel(InputsModel = InputsModelDown2,
+                                        RunOptions = RunOptionsDown,
+                                        InputsCrit = InputsCritDown,
+                                        CalibOptions = CalibOptionsDown,
                                         FUN_MOD = RunModel_GR4J)
 ParamDown2 <- OutputsCalibDown2$ParamFinalR
 ```
@@ -172,10 +180,14 @@ paste(format(Lag), "m/s")
 Both calibrations overestimate this parameter:
 
 ```{r}
-mLag <- matrix(c(Lag, OutputsCalibDown1$ParamFinalR[1], OutputsCalibDown2$ParamFinalR[1]), ncol = 1)
-rownames(mLag) = c("theoretical", "calibrated with observed upstream flow",
-                   "calibrated with simulated  upstream flow")
-colnames(mLag) = c("Lag parameter")
+mLag <- matrix(c(Lag,
+                 OutputsCalibDown1$ParamFinalR[1],
+                 OutputsCalibDown2$ParamFinalR[1]),
+               ncol = 1,
+               dimnames = list(c("theoretical",
+                                 "calibrated with observed upstream flow",
+                                 "calibrated with simulated  upstream flow"),
+                               c("Lag parameter")))
 knitr::kable(mLag)
 ```
 
@@ -197,11 +209,17 @@ CritDownTheo <- ErrorCrit_NSE(InputsCritDown, OutputsModelDownTheo)
 ## Parameters and performance of each subcatchment for all calibrations
 
 ```{r}
-comp <- matrix(c(0, OutputsCalibUp$ParamFinalR, rep(OutputsCalibDown1$ParamFinalR, 2),
-                 OutputsCalibDown2$ParamFinalR, ParamDownTheo), ncol = 5, byrow = TRUE)
-comp <- cbind(comp, c(OutputsCalibUp$CritFinal, OutputsCalibDown1$CritFinal,
-                      CritDown1$CritValue,  OutputsCalibDown2$CritFinal, CritDownTheo$CritValue))
-colnames(comp) <- c("Lag", paste0("x", 1:4), "NSE")
+comp <- matrix(c(0, OutputsCalibUp$ParamFinalR,
+                 rep(OutputsCalibDown1$ParamFinalR, 2),
+                 OutputsCalibDown2$ParamFinalR,
+                 ParamDownTheo),
+               ncol = 5, byrow = TRUE)
+comp <- cbind(comp, c(OutputsCalibUp$CritFinal,
+                      OutputsCalibDown1$CritFinal,
+                      CritDown1$CritValue,
+                      OutputsCalibDown2$CritFinal,
+                      CritDownTheo$CritValue))
+colnames(comp) <- c("Lag", paste0("X", 1:4), "NSE")
 rownames(comp) <- c("Calibration of the upstream subcatchment",
                     "Calibration 1 with observed upstream flow",
                     "Validation 1 with simulated upstream flow",
-- 
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