Development for v6.1.1

.github/workflows/check-standard.yml

@@ -21,7 +21,9 @@ on:
   pull_request:
     branches: [main, release/**]
 
-name: R-CMD-check
+name: R-CMD-check.yml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -33,7 +35,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -45,7 +47,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
 
@@ -72,4 +74,5 @@ jobs:
         with:
           upload-snapshots: true
           error-on: '"error"'
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
 

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "src/SOILWAT2"]
 	path = src/SOILWAT2
 	url = https://github.com/DrylandEcology/SOILWAT2
-	branch = master
+	branch = master

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: rSOILWAT2
-Version: 6.1.0
+Version: 6.1.1-9000
 Title: An Ecohydrological Ecosystem-Scale Water Balance Simulation Model
 Description: Access to the C-based SOILWAT2 v8.0.0 and functionality for
   SQLite-database of weather data.

NEWS.md

@@ -1,4 +1,11 @@
-# rSOILWAT2 v6.1.0-9000
+# rSOILWAT2 v6.1.1-9000
+* This version produces the same output as the previous version.
+
+## Bugfix
+* `dbW_fixWeather()` now handles data objects with all missing values.
+
+
+# rSOILWAT2 v6.1.0
 * This version produces the same output as the previous version.
 * `SOILWAT2` updated to v8.0.0 which now includes a simulation domain;
   however, this has no impact on `rSOILWAT2`.

R/swWeatherGenerator.R

@@ -1717,16 +1717,16 @@ dbW_fixWeather <- function(
   tmp <- which(rowSums(!is_miss1) > 0L)
   ids <- tmp[c(1L, length(tmp))]
 
-  ids_startend <-
+  ids_startend <- if (length(tmp) > 0L) {
     # before start
     (weatherData1[["Year"]] < weatherData1[ids[[1L]], "Year"]) |
-    (weatherData1[["Year"]] == weatherData1[ids[[1L]], "Year"] &
-        weatherData1[["DOY"]] < weatherData1[ids[[1L]], "DOY"]) |
-    # after end
-    (weatherData1[["Year"]] == weatherData1[ids[[2L]], "Year"] &
-        weatherData1[["DOY"]] > weatherData1[ids[[2L]], "DOY"]) |
-    (weatherData1[["Year"]] > weatherData1[ids[[2L]], "Year"])
-
+      (weatherData1[["Year"]] == weatherData1[ids[[1L]], "Year"] &
+          weatherData1[["DOY"]] < weatherData1[ids[[1L]], "DOY"]) |
+      # after end
+      (weatherData1[["Year"]] == weatherData1[ids[[2L]], "Year"] &
+          weatherData1[["DOY"]] > weatherData1[ids[[2L]], "DOY"]) |
+      (weatherData1[["Year"]] > weatherData1[ids[[2L]], "Year"])
+  }
 
 
   #--- Interpolate short missing runs

R/sw_Pedotransfer_Functions.R

@@ -1280,6 +1280,30 @@ check_swrcp <- function(swrc_name, swrcp) {
 #' awc <- diff(c(0, soils[, "depth_cm"])) * as.vector(diff(tmp))
 #'
 #'
+#' # Available water content "SWA" based on van Genuchten / Rosetta
+#' soils <- swSoils_Layers(rSOILWAT2::sw_exampleData)
+#' w <- diff(c(0, soils[, "depth_cm"]))
+#' vwc <- rbind(
+#'   day1 = rep(0.1, nrow(soils)),
+#'   day2 = rep(0.2, nrow(soils))
+#' )
+#' p <- ptf_estimate(
+#'   sand = soils[, "sand_frac"],
+#'   clay = soils[, "clay_frac"],
+#'   fcoarse = soils[, "gravel_content"],
+#'   bdensity = soils[, "bulkDensity_g/cm^3"],
+#'   swrc_name = "vanGenuchten1980",
+#'   ptf_name = "Rosetta3"
+#' )
+#' swa_base <- swrc_swp_to_vwc(
+#'   -3,
+#'   fcoarse = soils[, "gravel_content"],
+#'   swrc = list(name = "vanGenuchten1980", swrcp = p)
+#' )
+#' swa <- t(w * (t(vwc) - swa_base))
+#' swa[swa <= 0] <- 0 # SWA [cm / layer] above -3 MPa
+#'
+#'
 #' # Shape of SWRCs
 #' theta <- seq(0.05, 0.55, by = 0.001)
 #' soils <- data.frame(

README.md

@@ -106,15 +106,6 @@ Your computer must be set up adequately (see below for requirements).
     correctly install `rSOILWAT2` or explore one of the development branches.
 
 
-### Binary package
-If you require a binary version of the 'rSOILWAT2' package
-(e.g., to distribute to someone without development tools)
-for a platform to which you do not have access,
-then you may consider using one of the cloud services (no endorsements), e.g.,
-- [rhub](https://builder.r-hub.io) offers different
-  `Linux`, `Windows`, and `macOS` flavors as targets
-
-
 
 ### Minimal requirements
   - on any platform:

tests/testthat/test_WeatherGenerator_functionality.R

@@ -285,3 +285,40 @@ test_that("Weather generator (integration tests): compare input/output", {
     n = 5L
   )
 })
+
+
+test_that("Weather: fix dataset", {
+  #--- Check: fixedValue, interpolatedLienar, substituteData
+  x0 <- x <- dbW_weatherData_to_dataframe(rSOILWAT2::weatherData)
+
+   tmp <- x[, "Year"] == 1981
+   ids_to_interp <- tmp & x[, "DOY"] >= 144 & x[, "DOY"] <= 145
+   x[ids_to_interp, -(1:2)] <- NA
+
+   tmp <- x[, "Year"] == 1980
+   ids_to_sub <- tmp & x[, "DOY"] >= 153 & x[, "DOY"] <= 244
+   x[ids_to_sub, -(1:2)] <- NA
+
+   xf <- dbW_fixWeather(x, x0, return_weatherDF = TRUE)
+
+   expect_identical(
+     xf[["weatherData"]][!ids_to_interp, ],
+     as.data.frame(x0)[!ids_to_interp, ]
+   )
+
+   expect_gt(sum(!is.na(xf[["meta"]])), 0L)
+
+   expect_setequal(
+     names(table(xf[["meta"]])),
+     c("fixedValue", "interpolateLinear (<= 7 days)", "substituteData")
+   )
+
+
+   #--- Check: all values missing in - all values missing out
+   x <- dbW_weatherData_to_dataframe(rSOILWAT2::weatherData)
+   x[, weather_dataColumns()] <- NA
+
+   xf <- dbW_fixWeather(x, return_weatherDF = TRUE)
+   expect_true(all(is.na(x[, weather_dataColumns()])))
+   expect_identical(sum(!is.na(xf[["meta"]])), 0L)
+})