Doc update

NAMESPACE

@@ -1,7 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
+export(hurs2huss)
+export(hurs2w)
 export(huss2hurs)
 export(rad2cc)
+export(tas2ws)
 export(udConvertGrid)
 import(transformeR)
 importFrom(magrittr,"%<>%")

R/huss2hurs.R

@@ -29,6 +29,7 @@
 #' @importFrom magrittr %>% %<>% extract2
 #' @importFrom udunits2 ud.are.convertible
 #' @family derivation
+#' @template templateRefHumidity
 #' @examples
 #' data("ps.iberia")
 #' data("tas.iberia")
@@ -53,31 +54,32 @@ huss2hurs <- function(huss, ps, tas) {
     checkSeason(huss, ps, tas)
     # Check units
     u.huss <- getGridUnits(huss)
-    if (u.huss != "1") {
-        if (!ud.are.convertible(u.huss, "1")) {
-            stop("Non compliant huss units (should be convertible to \'1\')")
+    if (u.huss != "kg/kg") {
+        if (!ud.are.convertible(u.huss, "kg/kg")) {
+            stop("Non compliant huss units (should be convertible to \'kg/kg\')")
         }
-        message("Converting units ...")
-        huss <- udConvertGrid(huss, new.units = "1")
+        message("[", Sys.time(), "] Converting units ...")
+        huss <- udConvertGrid(huss, new.units = "kg/kg")
     }
     huss %<>% redim(member = TRUE)
     message("[", Sys.time(), "] Calculating Relative humidity ...")
     ws <- suppressMessages(tas2ws(tas, ps)) %>% redim(member = TRUE)
+    tas <- NULL
     coords <- getCoordinates(huss)
     n.mem <- getShape(huss, "member")
     l <- lapply(1:n.mem, function(x) {
         a <- subsetGrid(huss, members = x, drop = TRUE) %>% redim(member = FALSE) %>% extract2("Data") %>% array3Dto2Dmat()
         b <- subsetGrid(ws, members = x, drop = TRUE) %>% redim(member = FALSE) %>% extract2("Data") %>% array3Dto2Dmat()
-        w <- a/(1 - a) # w = mixing ratio
+        w <- a/(1 - a) # w = mixing (mass) ratio
         a <- 100 * w/b
-        huss$Data <- mat2Dto3Darray(a, x = coords$x, y = coords$y)
+        ps$Data <- mat2Dto3Darray(a, x = coords$x, y = coords$y)
         a <- b <- NULL
-        return(huss)
+        return(ps)
     })
-    tas <- ps <- huss <- NULL
+    huss <- ws <- ps <- NULL
     hurs <- suppressWarnings(bindGrid(l, dimension = "member"))
     hurs$Variable$varName <- "hurs"
-    hurs$Variable$level <- NULL
+    wt$Variable$level <- NULL
     attr(hurs$Variable, "units") <- "%"
     attr(hurs$Variable, "longname") <- "Surface_air_relative_humidity"
     attr(hurs$Variable, "description") <- "Estimated relative humidity from saturation pressure and specific humidity"

R/rad2cc.R

@@ -63,14 +63,14 @@ rad2cc <- function(rsds = NULL, rlds = NULL, rtds = NULL) {
             if (!ud.are.convertible(u1, "W.m-2")) {
                 stop("Non compliant rsds units (should be convertible to \'W.m-2\')")
             }
-            message("Converting units ...")
+            message("[", Sys.time(), "] Converting units ...")
             rsds <- udConvertGrid(rsds, new.units = "W.m-2") %>% redim(member = TRUE)
         }
         if (u2 != "W.m-2") {
             if (!ud.are.convertible(u2, "W.m-2")) {
                 stop("Non compliant rlds units (should be convertible to \'W.m-2\')")
             }
-            message("Converting units ...")
+            message("[", Sys.time(), "] Converting units ...")
             rlds <- udConvertGrid(rlds, new.units = "W.m-2") %>% redim(member = TRUE)
         }
         if (!is.null(rtds)) message("NOTE: rtds argument will be ignored, and calculated from rlds and rsds provided")
@@ -94,13 +94,15 @@ rad2cc <- function(rsds = NULL, rlds = NULL, rtds = NULL) {
     alpha <- matrix(90 + ref.coords[ ,2], ncol = nrow(ref.coords), nrow = length(jday), byrow = TRUE) - delta
     R0 <- 990 * sin(alpha * 2 * pi / 360) - 30
     n.mem <- getShape(rtds, "member")
+    cc <- rtds
     l <- lapply(1:n.mem, function(x) {
         tot.rad <- subsetGrid(rtds, members = x, drop = TRUE) %>% redim(member = FALSE) %>% extract2("Data") %>% array3Dto2Dmat()
         a <- suppressWarnings(exp(log((R0 - tot.rad) / (.75 * R0)) / 3.4))
         a[which(R0 - tot.rad < 0)] <- 0
-        rtds$Data <- mat2Dto3Darray(a, x = coords$x, y = coords$y)
-        return(rtds)
+        cc$Data <- mat2Dto3Darray(a, x = coords$x, y = coords$y)
+        return(cc)
     })
+    rtds <- NULL
     cc <- suppressWarnings(bindGrid(l, dimension = "member"))
     cc$Variable$varName <- "clt"
     cc$Variable$level <- NULL

R/tas2ws.R

@@ -20,20 +20,24 @@
 #' @description Calculates the saturation pressure using near-surface air temperature and surface pressure data
 #' @param tas Near-surface air temperature
 #' @param ps Surface pressure
-#' @return A climate4R grid of saturation pressure (in Pascals)
+#' @return A climate4R grid of saturation pressure (in atm)
 #' @author J. Bedia, S. Herrera
 #' @keywords internal
+#' @export
 #' @import transformeR
 #' @importFrom magrittr %>% %<>% extract2
 #' @importFrom udunits2 ud.are.convertible
 #' @template templateUnits
+#' @template templateRefHumidity
 #' @family derivation
-#' @examples \dontrun{
+#' @examples
 #' data("ps.iberia")
 #' data("tas.iberia")
 #' ws <- tas2ws(tas.iberia, ps.iberia)
-#' library(visualizeR)
-#' spatialPlot(climatology(ws), backdrop.theme = "coastline")}
+#' \dontrun{
+#' require(visualizeR)
+#' spatialPlot(climatology(ws), backdrop.theme = "coastline")
+#' }
 
 tas2ws <- function(tas, ps) {
     # Consistency checks:
@@ -53,20 +57,21 @@ tas2ws <- function(tas, ps) {
         if (!ud.are.convertible(u.ps, "Pa")) {
             stop("Non compliant ps units (should be convertible to \'Pascals')")
         }
-        message("Converting units ...")
+        message("[", Sys.time(), "] Converting units ...")
         ps <- udConvertGrid(ps, new.units = "Pa") %>% redim(member = TRUE)
     }
     if (u.tas != "K") {
         if (!ud.are.convertible(u.tas, "K")) {
             stop("Non compliant tas units (should be convertible to \'Kelvin\')")
         }
-        message("Converting units ...")
+        message("[", Sys.time(), "] Converting units ...")
         tas <- udConvertGrid(tas, new.units = "K") %>% redim(member = TRUE)
     }
-    message("Calculating saturation pressure ...")
+    message("[", Sys.time(), "] Calculating saturation pressure ...")
     source(file.path(find.package(package = "convertR"), "constants.R"), local = TRUE)
     coords <- getCoordinates(ps)
     n.mem <- getShape(tas, "member")
+    wt <- ps
     l <- lapply(1:n.mem, function(x) {
         a <- subsetGrid(tas, members = x, drop = TRUE) %>% redim(member = FALSE) %>% extract2("Data") %>% array3Dto2Dmat()
         b <- subsetGrid(ps, members = x, drop = TRUE) %>% redim(member = FALSE) %>% extract2("Data") %>% array3Dto2Dmat()
@@ -75,17 +80,17 @@ tas2ws <- function(tas, ps) {
         a[iceMask] <- es0 * exp((6293/T0) - (6293/a[iceMask]) - 0.555 * log(abs(a[iceMask]/T0)))
         a[waterMask] <- es0 * exp((6808/T0) - (6808/a[waterMask]) - 5.09 * log(abs(a[waterMask]/T0)))
         a <- (Rd/Rv) * (a/(b - a))
-        ps$Data <- mat2Dto3Darray(a, x = coords$x, y = coords$y)
+        wt$Data <- mat2Dto3Darray(a, x = coords$x, y = coords$y)
         a <- b <- NULL
-        return(ps)
+        return(wt)
     })
-    tas <- NULL
+    tas <- ps <- NULL
     wt <- suppressWarnings(bindGrid(l, dimension = "member"))
     wt$Variable$varName <- "ws"
     wt$Variable$level <- NULL
-    attr(wt$Variable, "units") <- "Pa"
-    attr(wt$Variable, "longname") <- "Saturation_pressure"
-    attr(wt$Variable, "description") <- "Estimated saturation pressure"
-    message("Done")
+    attr(wt$Variable, "units") <- "atm"
+    attr(wt$Variable, "longname") <- "Vapour_pressure_of_water"
+    attr(wt$Variable, "description") <- "The vapour pressure of water is the pressure at which water vapour is in thermodynamic equilibrium with its condensed state"
+    message("[", Sys.time(), "] Done.")
     invisible(wt)
 }

inst/constants.R

@@ -3,4 +3,4 @@ Rd <- 287.058 # dry air constant J/(K kg)
 epsilon <- Rd/Rv # adimensional
 T0 <- 273.15 # K
 es0 <- 611 # Pa
-GammaST <- .0065 # (dT/dz)^st standard atmosphere vertical gradient of the temperature in the troposphere (0.0065 (K/m^-1))
+GammaST <- 6.5e-03 # (dT/dz)^st standard atmosphere vertical gradient of the temperature in the troposphere (0.0065 (K/m^-1))