Feature improve weather (#244)

- functionality to impute and 'fix' weather
- functionality to download weather and format for rSOILWAT2

NAMESPACE

@@ -44,6 +44,7 @@ export(dbW_deleteSiteData)
 export(dbW_delete_duplicated_weatherData)
 export(dbW_disconnectConnection)
 export(dbW_estimate_WGen_coefs)
+export(dbW_fixWeather)
 export(dbW_generateWeather)
 export(dbW_getIDs)
 export(dbW_getScenarioId)
@@ -57,7 +58,9 @@ export(dbW_has_siteIDs)
 export(dbW_has_sites)
 export(dbW_has_weatherData)
 export(dbW_have_sites_all_weatherData)
+export(dbW_imputeWeather)
 export(dbW_setConnection)
+export(dbW_substituteWeather)
 export(dbW_updateSites)
 export(dbW_upgrade_to_rSOILWAT2)
 export(dbW_upgrade_v1to2)
@@ -138,6 +141,8 @@ export(sw_dailyC4_TempVar)
 export(sw_exec)
 export(sw_inputData)
 export(sw_inputDataFromFiles)
+export(sw_meteo_obtain_DayMet)
+export(sw_meteo_obtain_SCAN)
 export(sw_out_flags)
 export(sw_outputData)
 export(sw_verbosity)
@@ -148,6 +153,7 @@ export(swrc_vwc_to_swp)
 export(time_columns)
 export(update_biomass)
 export(update_requested_years)
+export(upgrade_weatherDF)
 export(upgrade_weatherHistory)
 export(weatherGenerator_dataColumns)
 export(weatherHistory)

NEWS.md

@@ -1,4 +1,38 @@
 # rSOILWAT2 v6.0.4-9000
+* This version produces the same output as the previous version.
+
+## New features
+* New `upgrade_weatherDF()` adds requested weather columns to a data frame
+  (@dschlaep).
+* Improved rounding of weather functionality (@dschlaep):
+    * `dbW_weatherData_round()` now rounds both `"weatherList"` and
+      `"weatherDF"` objects; argument `"digits"` can now also be logical
+      (if `TRUE`, then digits takes the default value of 4) or not finite
+      (e.g., `NA`; not finite values return the input without rounding).
+    * Argument `"round"` of `dbW_dataframe_to_weatherData()` is deprecated and
+      changed the default value from rounding to 2 digits to no rounding (`NA`);
+      recommended replacement is a separate call to `dbW_weatherData_round()`.
+    * Argument `"digits"` of `dbW_generateWeather()` changed the default value
+      from rounding to 4 digits to no rounding (`NA`).
+* `dbW_generateWeather()` gained `"return_weatherDF"` and now returns a
+  user requested weather object type (@dschlaep).
+  If `return_weatherDF` is `TRUE`, then the result is converted to a
+  data frame where columns represent weather variables; otherwise,
+  a list of elements of class `swWeatherData` is returned (as previously).
+* New `dbW_imputeWeather()` replaces missing weather values using
+  using the weather generator and
+  using functionality by `rSW2utils::impute_df()` (@dschlaep).
+* New `dbW_substituteWeather()` replaces missing weather values in one
+  weather data object with values from a second weather data object (@dschlaep).
+* New `dbW_fixWeather()` fixes missing weather values using a sequence of
+  approaches including linear interpolation for short missing spells,
+  a fixed value for short spells of missing precipitation (optionally),
+  substitution from a second weather data object, and
+  replacement with long term daily mean values (@dschlaep).
+* New family of functions `sw_meteo_obtain` that obtain (download) weather
+  data from external sources and prepare for use by `"rSOILWAT2"` (@dschlaep):
+      * New `sw_meteo_obtain_DayMet()` obtains and formats data from `"Daymet"`
+      * New `sw_meteo_obtain_SCAN()` obtains and formats data from `"SCAN"`
 
 
 # rSOILWAT2 v6.0.3

R/A_swGenericMethods.R

@@ -230,7 +230,7 @@ format_timestamp <- function(object) {
 #'         `"SWA"` added as `outkey` 8 for a new total of 30
 #'
 #' @examples
-#'   x <- sw_upgrade(rSOILWAT2::sw_exampleData, verbose = TRUE)
+#' x <- sw_upgrade(rSOILWAT2::sw_exampleData, verbose = TRUE)
 #'
 #' @md
 #' @exportMethod sw_upgrade

R/D_swWeatherData.R

@@ -188,12 +188,42 @@ swWeatherData <- function(...) {
   do.call("new", args = c("swWeatherData", dots[dns %in% sns]))
 }
 
+#' @param weatherDF A data frame with weather variables.
+#' @param template_weatherColumns A vector with requested weather variables.
+#'
+#' @return For [upgrade_weatherDF()]:
+#' an updated `weatherDF` with requested columns.
+#'
+#' @examples
+#' upgrade_weatherDF(
+#'   data.frame(DOY = 1:2, Tmax_C = runif(2), dummy = runif(2))
+#' )
+#'
+#' @md
+#' @rdname sw_upgrade
+#' @export
+upgrade_weatherDF <- function(
+  weatherDF,
+  template_weatherColumns = c("Year", "DOY", weather_dataColumns())
+) {
+  template_data <- as.data.frame(
+    array(
+      dim = c(nrow(weatherDF), length(template_weatherColumns)),
+      dimnames = list(NULL, template_weatherColumns)
+    )
+  )
+
+  cns <- intersect(template_weatherColumns, colnames(weatherDF))
+  if (length(cns) < 1L) stop("Required weather variables not found.")
+  template_data[, cns] <- weatherDF[, cns]
+  template_data
+}
 
 upgrade_swWeatherData <- function(data, year, template = new("swWeatherData")) {
-  stopifnot(colnames(data) %in% colnames(template@data))
   template@year <- as.integer(year)
-  template@data <- template@data[seq_len(nrow(data)), , drop = FALSE]
-  template@data[, colnames(data)] <- data
+  template@data <- data.matrix(
+    upgrade_weatherDF(data, c("DOY", weather_dataColumns()))
+  )
   template
 }