Read more daily input

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "src/SOILWAT2"]
 	path = src/SOILWAT2
 	url = https://github.com/DrylandEcology/SOILWAT2
-	branch = release/devel_v7.0.0
+	branch = read_more_daily_input

NAMESPACE

@@ -16,6 +16,7 @@ export(calc_RRs_Chambers2014)
 export(calc_RRs_Maestas2016)
 export(calc_SMTRs)
 export(calc_SiteClimate)
+export(calc_dailyInputFlags)
 export(check_SWRC_vs_PTF)
 export(check_TranspirationRegions)
 export(check_ptf_availability)
@@ -84,6 +85,7 @@ export(get_version)
 export(get_years_from_weatherDF)
 export(get_years_from_weatherData)
 export(has_soilTemp_failed)
+export(is_missing_weather)
 export(list_matched_swrcs_ptfs)
 export(lookup_annual_CO2a)
 export(nrow_output)
@@ -146,7 +148,11 @@ export(swrc_vwc_to_swp)
 export(time_columns)
 export(update_biomass)
 export(update_requested_years)
+export(upgrade_weatherHistory)
+export(weatherGenerator_dataColumns)
 export(weatherHistory)
+export(weather_dataAggFun)
+export(weather_dataColumns)
 exportClasses(swCarbon)
 exportClasses(swCloud)
 exportClasses(swEstab)

NEWS.md

@@ -4,12 +4,16 @@
 * `SOILWAT2` updated to v7.0.0
 * This version produces nearly identical simulation output
   as the previous release under default values.
-  Small deviations arise due to a fix in the handling of soil moisture values
-  between field capacity and saturation.
+  Small deviations arise due to
+    1. a fix in the handling of soil moisture values
+       between field capacity and saturation;
+    2. a fix in the calculation of potential natural vegetation; and
+    3. a fix in the calculation of climate variables (if used).
 
 ## New features
 * New method `sw_upgrade()` upgrades objects with
-  outdated `rSOILWAT2` S4 classes to the current version.
+  outdated `rSOILWAT2` S4 classes to the current version;
+  new `upgrade_weatherHistory()` upgrades outdated weather history objects.
 * New `get_soilmoisture()` to consistently extract soil moisture content,
   volumetric water content (bulk soil), or
   volumetric water content for the matric component.
@@ -21,6 +25,21 @@
 * New `time_columns()` returns the output column indices with time information.
 * New `nrow_output()` returns the number of time steps in output.
 
+* Daily weather inputs, in addition to the previous variables
+  maximum air temperature, minimum air temperature, and precipitation amount,
+  can now process the following variables (issue #229; @dschlaep, @N1ckP3rsl3y):
+    * Cloud cover (can be replaced by shortwave radiation)
+    * Wind speed (can be replaced by wind components)
+    * Wind speed eastward component (optional)
+    * Wind speed northward component (optional)
+    * Relative humidity (can be replaced by max/min humidity, specific humidity
+      dew point temperature, or vapor pressure)
+    * Maximum relative humidity (optional)
+    * Minimum relative humidity (optional)
+    * Specific humidity (optional)
+    * Dew point temperature (optional)
+    * Actual vapor pressure (optional)
+    * Downward surface shortwave radiation (optional)
 
 * This version now handles a variety of soil water retention curves `SWRC`
   and pedotransfer functions `PTF` (issue #207, @dschlaep).
@@ -94,7 +113,15 @@
   as inputs (value 0, as previously).
 * `SWPtoVWC()` and `VWCtoSWP()` are deprecated in favor of
   `swrc_swp_to_vwc()` and `swrc_vwc_to_swp()` respectively.
-
+* Class `swWeather` gains new slots (issue #229)
+    * `"use_cloudCoverMonthly"`, `"use_windSpeedMonthly"`, and
+      `"use_humidityMonthly"` which determine whether mean monthly values
+      (from `swCloud`) or daily values (from `swWeatherData`) are utilized;
+    * `"dailyInputFlags"` which indicates which of the 14 possible daily
+      weather variables are present in the inputs;
+    * `"desc_rsds"` which describes units of input shortwave radiation.
+* Class `swWeatherData` gains new columns in slot `"data"` that accommodate
+  all 14 possible daily weather variables (issue #229).
 
 # rSOILWAT2 v5.4.1
 * This version produces identical simulation output as the previous release.

R/A_swGenericMethods.R

@@ -48,6 +48,8 @@ rSW2_version <- function() {
 #' @examples
 #' get_version(rSOILWAT2::sw_exampleData)
 #' get_version(sw_exec(rSOILWAT2::sw_exampleData))
+#' get_version(as.numeric_version("4.1.3"))
+#' get_version(packageVersion("rSOILWAT2"))
 #'
 #' @export
 setGeneric("get_version", function(object) standardGeneric("get_version"))
@@ -57,11 +59,16 @@ setMethod(
   "get_version",
   signature = "ANY",
   definition = function(object) {
-    tmp <- try(object@version, silent = TRUE)
-    if (inherits(tmp, "try-error")) {
-      NA_character_
+    tmp <- try(inherits(object, "numeric_version"), silent = TRUE)
+    if (inherits(tmp, "try-error") || !isTRUE(tmp)) {
+      tmp <- try(object@version, silent = TRUE)
+      if (inherits(tmp, "try-error")) {
+        NA_character_
+      } else {
+        as.character(as.numeric_version(tmp))
+      }
     } else {
-      as.character(as.numeric_version(tmp))
+      as.character(object) # numeric version
     }
   }
 )

R/D_swWeather.R

@@ -57,10 +57,10 @@ setClass(
   prototype = list(
     MonthlyScalingParams = array(
       NA_real_,
-      dim = c(12, 6),
+      dim = c(12, 8),
       dimnames = list(
         NULL,
-        c("PPT", "MaxT", "MinT", "SkyCover", "Wind", "rH")
+        c("PPT", "MaxT", "MinT", "SkyCover", "Wind", "rH", "ActVP", "ShortWR")
       )
     )
   )
@@ -72,10 +72,10 @@ setValidity(
     val <- TRUE
     temp <- dim(object@MonthlyScalingParams)
 
-    if (temp[2] != 6) {
+    if (temp[2] != 8) {
       msg <- paste(
-        "@MonthlyScalingParams must have exactly 6 columns ",
-        "corresponding to PPT, MaxT, MinT, SkyCover, Wind, rH"
+        "@MonthlyScalingParams must have exactly 8 columns ",
+        "corresponding to PPT, MaxT, MinT, SkyCover, Wind, rH, ActVP, ShortWR"
       )
       val <- if (isTRUE(val)) msg else c(val, msg)
     }
@@ -120,6 +120,52 @@ swMonthlyScalingParams <- function(...) {
   do.call("new", args = c("swMonthlyScalingParams", tmp))
 }
 
+sw_upgrade_MonthlyScalingParams <- function( # nolint: object_length_linter.
+  MonthlyScalingParams,
+  verbose = FALSE
+) {
+  if (verbose) {
+    message("Upgrading object `MonthlyScalingParams`.")
+  }
+
+  #--- Add new columns (use default values)
+  default <- swMonthlyScalingParams()
+  vars_exp <- colnames(default@MonthlyScalingParams)
+  vars_has <- colnames(MonthlyScalingParams)
+
+  if (!all(vars_exp %in% vars_has)) {
+    res <- default@MonthlyScalingParams
+    res[, vars_has] <- MonthlyScalingParams[, vars_has]
+    res
+  } else {
+    MonthlyScalingParams
+  }
+}
+
+
+#' @rdname sw_upgrade
+setMethod(
+  "sw_upgrade",
+  signature = "swMonthlyScalingParams",
+  definition = function(object, verbose = FALSE) {
+    tmp <- try(validObject(object), silent = TRUE)
+    if (inherits(tmp, "try-error")) {
+      if (verbose) {
+        message("Upgrading object of class `swMonthlyScalingParams`.")
+      }
+
+      object@MonthlyScalingParams <- suppressWarnings(
+        sw_upgrade_MonthlyScalingParams(object@MonthlyScalingParams)
+      )
+
+      #--- Check validity and return
+      validObject(object)
+    }
+
+    object
+  }
+)
+
 
 
 #####################WEATHERSETUP.IN###################################
@@ -163,7 +209,12 @@ setClass(
     pct_SnowRunoff = "numeric",
     use_weathergenerator = "logical",
     use_weathergenerator_only = "logical",
-    FirstYear_Historical = "integer"
+    FirstYear_Historical = "integer",
+    use_cloudCoverMonthly = "logical",
+    use_windSpeedMonthly = "logical",
+    use_humidityMonthly = "logical",
+    desc_rsds = "integer",
+    dailyInputFlags = "logical"
   ),
   # TODO: this class should not contain `swMonthlyScalingParams` but
   # instead be a composition, i.e., have a slot of that class
@@ -174,7 +225,14 @@ setClass(
     pct_SnowRunoff = NA_real_,
     use_weathergenerator = NA,
     use_weathergenerator_only = NA,
-    FirstYear_Historical = NA_integer_
+    FirstYear_Historical = NA_integer_,
+    use_cloudCoverMonthly = NA,
+    use_windSpeedMonthly = NA,
+    use_humidityMonthly = NA,
+    desc_rsds = NA_integer_,
+    # NOTE: 14 must be
+    # equal to rSW2_glovars[["kSOILWAT2"]][["kINT"]][["MAX_INPUT_COLUMNS"]]
+    dailyInputFlags = rep(NA, 14L)
   )
 )
 
@@ -185,8 +243,18 @@ setValidity(
     sns <- setdiff(slotNames("swWeather"), inheritedSlotNames("swWeather"))
 
     for (sn in sns) {
-      if (length(slot(object, sn)) != 1) {
-        msg <- paste0("@", sn, " must have exactly one value.")
+      n_exp <- if (sn %in% "dailyInputFlags") {
+        rSW2_glovars[["kSOILWAT2"]][["kINT"]][["MAX_INPUT_COLUMNS"]]
+      } else {
+        1L
+      }
+
+      n_has <- length(slot(object, sn))
+
+      if (n_has != n_exp) {
+        msg <- paste0(
+          "@", sn, " has n = ", n_has, " instead of n = ", n_exp, " value(s)."
+        )
         val <- if (isTRUE(val)) msg else c(val, msg)
       }
     }
@@ -233,6 +301,36 @@ swWeather <- function(...) {
 }
 
 
+
+
+#' @rdname sw_upgrade
+setMethod(
+  "sw_upgrade",
+  signature = "swWeather",
+  definition = function(object, verbose = FALSE) {
+    tmp <- try(validObject(object), silent = TRUE)
+    if (inherits(tmp, "try-error")) {
+      # Upgrade `MonthlyScalingParams` with dedicated upgrade method first;
+      # `swMonthlyScalingParams()` via `swWeather()` cannot handle
+      # an increased number of columns in `MonthlyScalingParams` otherwise
+      object@MonthlyScalingParams <- suppressWarnings(
+        sw_upgrade_MonthlyScalingParams(
+          object@MonthlyScalingParams,
+          verbose = verbose
+        )
+      )
+
+      if (verbose) {
+        message("Upgrading object of class `swWeather`.")
+      }
+      object <- suppressWarnings(swWeather(object))
+    }
+
+    object
+  }
+)
+
+
 #' @rdname swWeather-class
 #' @export
 setMethod(
@@ -427,14 +525,22 @@ setMethod(
     object@pct_SnowRunoff <- readNumeric(infiletext[6])
     object@use_weathergenerator <- readLogical(infiletext[7])
     object@FirstYear_Historical <- readInteger(infiletext[8])
+    object@use_cloudCoverMonthly <- readLogical(infiletext[9])
+    object@use_windSpeedMonthly <- readLogical(infiletext[10])
+    object@use_relHumidityMonthly <- readLogical(infiletext[11])
+    object@desc_rsds <- readLogical(infiletext[12])
+
+    for (i in seq_len(14)) {
+      object@dailyInputFlags[i] <- readLogical(infiletext[12 + 1])
+    }
 
-    data <- matrix(data = c(rep(1, 12), rep(NA, 12 * 5)), nrow = 12, ncol = 6)
-    colnames(data) <- c("PPT", "MaxT", "MinT", "SkyCover", "Wind", "rH")
+    data <- matrix(data = c(rep(1, 12), rep(NA, 12 * 5)), nrow = 12, ncol = 8)
+    colnames(data) <- c("PPT", "MaxT", "MinT", "SkyCover", "Wind", "rH", "actVP", "shortWR")
     rownames(data) <- c("January", "February", "March", "April", "May",
       "June", "July", "August", "September", "October", "November", "December")
 
-    for (i in 21:32) {
-      data[i - 20, ] <- readNumerics(infiletext[i], 8)[2:8]
+    for (i in 1:12) {
+      data[i, ] <- readNumerics(infiletext[12 + 14 + i], 8)[2:8]
     }
     object@MonthlyScalingParams <- data