From 68ce1825e431196427ee55db7f4e2a7792620afa Mon Sep 17 00:00:00 2001
From: Dorchies David <david.dorchies@inrae.fr>
Date: Wed, 24 Mar 2021 10:53:52 +0100
Subject: [PATCH] feat(Lag): allow NAs in Qupstream
Refs #100
---
R/CreateInputsModel.R | 2 +-
R/RunModel_Lag.R | 14 +++++++---
tests/testthat/test-RunModel_Lag.R | 42 ++++++++++++++++++------------
vignettes/V05_sd_model.Rmd | 13 +++------
4 files changed, 41 insertions(+), 30 deletions(-)
diff --git a/R/CreateInputsModel.R b/R/CreateInputsModel.R
index 2a2a6488..3bd0f147 100644
--- a/R/CreateInputsModel.R
+++ b/R/CreateInputsModel.R
@@ -210,7 +210,7 @@ CreateInputsModel <- function(FUN_MOD,
stop("'Qupstream' must have same number of rows as 'DatesR' length")
}
if(any(is.na(Qupstream))) {
- stop("'Qupstream' cannot contain any NA value")
+ 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 v1.7 of airGR: values superior to 1000 km seem unrealistic")
diff --git a/R/RunModel_Lag.R b/R/RunModel_Lag.R
index 9344a78b..e98e1b86 100644
--- a/R/RunModel_Lag.R
+++ b/R/RunModel_Lag.R
@@ -83,10 +83,16 @@ RunModel_Lag <- function(InputsModel, RunOptions, Param) {
Qupstream[2:(1 + LengthTs)] * HUTRANS[1, upstream_basin] +
Qupstream[1:LengthTs] * HUTRANS[2, upstream_basin]
}
- # Warning for negative flows
- if (any(OutputsModel$Qsim < 0)) {
- warning(length(which(OutputsModel$Qsim < 0)), " time steps with negative flow, set to zero.")
- OutputsModel$Qsim[OutputsModel$Qsim < 0] <- 0
+ # Warning for negative flows or NAs only in extended outputs
+ if(length(RunOptions$Outputs_Sim <3)) {
+ if (any(OutputsModel$Qsim[!is.na(OutputsModel$Qsim)] < 0)) {
+ warning(length(which(OutputsModel$Qsim < 0)), " time steps with negative flow, set to zero.")
+ OutputsModel$Qsim[OutputsModel$Qsim < 0] <- 0
+ }
+ # Warning for NAs
+ if (any(is.na(OutputsModel$Qsim))) {
+ warning(length(which(is.na(OutputsModel$Qsim))), " time steps with NA values")
+ }
}
# Convert back Qsim to mm
OutputsModel$Qsim <- OutputsModel$Qsim / sum(InputsModel$BasinAreas, na.rm = TRUE) / 1e3
diff --git a/tests/testthat/test-RunModel_Lag.R b/tests/testthat/test-RunModel_Lag.R
index 179bd87e..b3eca041 100644
--- a/tests/testthat/test-RunModel_Lag.R
+++ b/tests/testthat/test-RunModel_Lag.R
@@ -19,21 +19,6 @@ test_that("'BasinAreas' must have one more element than 'LengthHydro'", {
BasinAreas <- c(BasinInfo$BasinArea, BasinInfo$BasinArea)
-test_that("'Qupstream' cannot contain any NA value", {
- expect_error(
- InputsModel <- CreateInputsModel(
- FUN_MOD = RunModel_GR4J,
- DatesR = BasinObs$DatesR,
- Precip = BasinObs$P,
- PotEvap = BasinObs$E,
- Qupstream = matrix(BasinObs$Qmm, ncol = 1),
- LengthHydro = 1,
- BasinAreas = BasinAreas
- ),
- regexp = "'Qupstream' cannot contain any NA value"
- )
-})
-
# Qupstream = sinusoid synchronised on hydrological year from 0 mm to mean value of Qobs
Qupstream <- floor((sin((seq_along(BasinObs$Qmm)/365*2*3.14))+1) * mean(BasinObs$Qmm, na.rm = TRUE))
@@ -85,7 +70,7 @@ test_that("'InputsModel$OutputsModel$Qim' should have the same lenght as 'RunOpt
)
})
-test_that("'InputsModel$OutputsModel$Qim' should contain no NA'", {
+test_that("'InputsModel$OutputsModel$Qsim' should contain no NA'", {
InputsModel$OutputsModel <- OutputsGR4JOnly
InputsModel$OutputsModel$Qsim[10L] <- NA
expect_error(
@@ -94,6 +79,31 @@ test_that("'InputsModel$OutputsModel$Qim' should contain no NA'", {
)
})
+test_that("'Qupstream' contain NA values", {
+ expect_warning(
+ InputsModel <- CreateInputsModel(
+ FUN_MOD = RunModel_GR4J,
+ DatesR = BasinObs$DatesR,
+ Precip = BasinObs$P,
+ PotEvap = BasinObs$E,
+ Qupstream = matrix(BasinObs$Qmm, ncol = 1),
+ LengthHydro = 1,
+ BasinAreas = BasinAreas
+ ),
+ regexp = "'Qupstream' contains NA values: model outputs will contain NAs"
+ )
+
+ RunOptions <- suppressWarnings(CreateRunOptions(FUN_MOD = RunModel_GR4J,
+ InputsModel = InputsModel,
+ IndPeriod_Run = Ind_Run))
+ InputsModel$OutputsModel <- OutputsGR4JOnly
+
+ expect_warning(
+ RunModel_Lag(InputsModel = InputsModel, RunOptions = RunOptions, Param = 1),
+ regexp = "time steps with NA values"
+ )
+})
+
test_that("Upstream basin with nil area should return same Qdown as GR4J alone", {
UpstBasinArea <- InputsModel$BasinAreas[1L]
InputsModel$BasinAreas[1L] <- 0
diff --git a/vignettes/V05_sd_model.Rmd b/vignettes/V05_sd_model.Rmd
index 430c8e3b..632819c1 100644
--- a/vignettes/V05_sd_model.Rmd
+++ b/vignettes/V05_sd_model.Rmd
@@ -12,7 +12,6 @@ vignette: >
```{r, include=FALSE, fig.keep='none', results='hide'}
library(airGR)
options(digits = 3)
-library(imputeTS)
```
# Introduction
@@ -56,7 +55,9 @@ For the observed flow at the downstream outlet, we generate it with the assumpti
```{r}
QObsDown <- (BasinObs$Qmm + c(0, 0, BasinObs$Qmm[1:(length(BasinObs$Qmm)-2)])) / 2
-summary(cbind(QObsUp = BasinObs$Qmm, QObsDown), digits = 3)
+options(digits = 5)
+summary(cbind(QObsUp = BasinObs$Qmm, QObsDown))
+options(digits = 3)
```
# Calibration of the upstream subcatchment
@@ -91,19 +92,13 @@ OutputsModelUp <- RunModel_GR4J(InputsModel = InputsModelUp, RunOptions = RunOpt
# Calibration of the downstream subcatchment with upstream flow observations
-Observed flow data contain `NA` values and a complete time series is mandatory for running the Lag model. We propose to complete the observed upstream flow with linear interpolation:
-
-```{r}
-QObsUp <- imputeTS::na_interpolation(BasinObs$Qmm)
-```
-
we need to create the `InputsModel` object completed with upstream information:
```{r}
InputsModelDown1 <- CreateInputsModel(
FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR,
Precip = BasinObs$P, PotEvap = BasinObs$E,
- Qupstream = matrix(QObsUp, ncol = 1), # upstream observed flow
+ Qupstream = matrix(BasinObs$Qmm, ncol = 1), # upstream observed flow
LengthHydro = 100, # distance between upstream catchment outlet & the downstream one [km]
BasinAreas = c(180, 180) # upstream and downstream areas [km²]
)
--
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