Doc update

DESCRIPTION

@@ -21,11 +21,11 @@ Suggests:
     visualizeR
 Type: Package
 Title: An R package for climate data manipulation and transformation
-Version: 1.3.3
-Date: 2018-04-24
+Version: 1.4.0
+Date: 2018-06-08
 Authors@R: as.person(c(
     "Santander Meteorology Group <http://meteo.unican.es> [cph]",
-    "Jorge Bano Medina <bmedina@ifca.unican.es> [ctb]",
+    "Jorge Baño Medina <bmedina@ifca.unican.es> [ctb]",
     "Joaquin Bedia <bediaj@unican.es> [aut, cre]",
     "Matteo De Felice <matteo.defelice@enea.it> [ctb]",
     "Jose Manuel Gutierrez <gutierjm@unican.es> [ctb]",

NEWS

@@ -1,9 +1,8 @@
-transformeR 1.3.3
+transformeR 1.4.0
 =================
 
-* Renamed `localScaling` to `scaleGrid`
-* Update variable names/levels in built-in datasets for consistency (NCEP, CMIP5)
-* Other minor doc updates and internal changes
+* New function `intersectGrid`, for calculating spatiotemporal intersections among grids
+* Optional flag to skip seasonal check in `scaleGrid`
 
 
 

R/intersectGrid.R

@@ -8,12 +8,12 @@
 #' @family subsetting
 #' @seealso \code{\link{subsetGrid}}
 #' @export
-#' @example {
-# data("EOBS_Iberia_tas")
-# a <- subsetGrid(EOBS_Iberia_tas, lonLim = c(-8,-1), latLim = c(37, 40))
-# b <- subsetGrid(EOBS_Iberia_tas, lonLim = c(-4,3), latLim = c(39, 43))
-# z <- intersectGrid(a, b, type = "spatial", which.return = 1)
-# }
+#' @examples {
+#' data("EOBS_Iberia_tas")
+#' a <- subsetGrid(EOBS_Iberia_tas, lonLim = c(-8,-1), latLim = c(37, 40))
+#' b <- subsetGrid(EOBS_Iberia_tas, lonLim = c(-4,3), latLim = c(39, 43))
+#' z <- intersectGrid(a, b, type = "spatial", which.return = 1)
+#' }
 
 intersectGrid <- function(..., type = c("temporal", "spatial"), which.return = 1) {
       type <- match.arg(type, choices = c("temporal", "spatial"))

R/overGrid.R

@@ -15,27 +15,8 @@
 #' 
 #' @return A grid
 #' @author M. Iturbide
+#' @family subsetting
 #' @export
-#' @examples
-#' library(visualizeR)
-#' data("PRUDENCEregions")
-#' library(loadeR)
-#' grid <- loadGridData(
-#'       "http://opendap.knmi.nl/knmi/thredds/dodsC/e-obs_0.25regular/tx_0.25deg_reg_v17.0.nc",
-#'       var = "tx", years = 1983, season = 12)
-#' 
-#' iberia <- overGrid(grid, PRUDENCEregions[2, ])
-#' iberia2 <- overGrid(grid, PRUDENCEregions[2,], subset = TRUE)
-#' allregions <- overGrid(grid, PRUDENCEregions, subset = TRUE)
-#' 
-#' spatialPlot(climatology(grid),
-#'             sp.layout = list(list(PRUDENCEregions, first = FALSE)))
-#' spatialPlot(climatology(iberia),
-#'             sp.layout = list(list(PRUDENCEregions, first = FALSE)))
-#' spatialPlot(climatology(iberia2),
-#'             sp.layout = list(list(PRUDENCEregions, first = FALSE)))
-#' spatialPlot(climatology(allregions),
-#'             sp.layout = list(list(PRUDENCEregions, first = FALSE)))
 
 
 overGrid <- function(grid, layer, subset = FALSE) {
@@ -44,7 +25,6 @@ overGrid <- function(grid, layer, subset = FALSE) {
       # grid <- redim(grid, runtime = TRUE)
       loc <- "loc" %in% getDim(grid)
       grid <- redim(grid, loc = loc)
-      dimNames <- getDim(grid)
       # n.run <- getShape(grid)["runtime"]
       n.mem <- getShape(grid)["member"]
       if (loc) {

R/scaleGrid.R

@@ -38,6 +38,9 @@
 #'  and \code{"daily"}, for a julian day-based approach. See details.
 #' @param type Character string. Either \code{"center"}, \code{"standardize"} or \code{"ratio"}, depending on wheter the correction factor are anomalies (e.g. temperature...),
 #' estandardized anomalies or applied as a ratio (e.g. precipitation, wind speed...). See details
+#' @param skip.season.check Logical flag. Should the internal checker \code{\link{checkSeason}} be skipped?. By
+#' default, the function undertakes an automatic seasonal check. This can be skipped if needed, mainly for internal use
+#' (e.g. in cross-validation setups)
 #'   
 #' @template templateParallelParams
 #' @details In the \code{type = "center"} set up the reference grid (\code{ref}) is used to correct the input grid, as follows:
@@ -177,13 +180,15 @@ scaleGrid <- function(grid,
                       type = "center",
                       parallel = FALSE,
                       max.ncores = 16,
-                      ncores = NULL) {
+                      ncores = NULL,
+                      skip.season.check = FALSE) {
     time.frame <- match.arg(time.frame, choices = c("none", "monthly", "daily"))
     type <- match.arg(type, choices = c("center", "standardize", "ratio"))
     spatial.frame <- match.arg(spatial.frame, choices = c("gridbox", "field"))
+    stopifnot(is.logical(skip.season.check))
     if (time.frame == "none") {
         message("[", Sys.time(), "] - Scaling ...")
-        out <- gridScale.(grid, base, ref, clim.fun, by.member, type, parallel, max.ncores, ncores, spatial.frame)
+        out <- gridScale.(grid, base, ref, clim.fun, by.member, type, parallel, max.ncores, ncores, spatial.frame, skip.season.check)
         message("[", Sys.time(), "] - Done")
     } else if (time.frame == "monthly") {
         message("[", Sys.time(), "] - Scaling by months ...")
@@ -200,7 +205,7 @@ scaleGrid <- function(grid,
             } else {
                 NULL
             }
-            gridScale.(grid1, base1, ref1, clim.fun, by.member, type, parallel, max.ncores, ncores, spatial.frame)
+            gridScale.(grid1, base1, ref1, clim.fun, by.member, type, parallel, max.ncores, ncores, spatial.frame, skip.season.check)
         })
         out <- do.call("bindGrid.time", aux.list)
         message("[", Sys.time(), "] - Done")
@@ -245,7 +250,8 @@ scaleGrid <- function(grid,
 #' @importFrom parallel stopCluster
 #' @author J Bedia
 
-gridScale. <- function(grid, base, ref, clim.fun, by.member, type, parallel, max.ncores, ncores, spatial.frame) {
+gridScale. <- function(grid, base, ref, clim.fun, by.member, type, parallel, max.ncores, ncores,
+                       spatial.frame, skip.season.check) {
   grid <- redim(grid)
   if (is.null(base)) {
     base.m <- suppressMessages({
@@ -269,7 +275,7 @@ gridScale. <- function(grid, base, ref, clim.fun, by.member, type, parallel, max
     }
 
   } else {
-    # checkSeason(grid, base)
+    if (!skip.season.check) checkSeason(grid, base)
     checkDim(grid, base, dimensions = c("lat", "lon"))
     base.m <- suppressMessages({
       climatology(base, clim.fun, by.member, parallel, max.ncores, ncores)
@@ -293,7 +299,7 @@ gridScale. <- function(grid, base, ref, clim.fun, by.member, type, parallel, max
   }
   if (!is.null(ref)) {
     checkDim(grid, ref, dimensions = c("lat", "lon"))
-    # checkSeason(grid, ref)
+    if (!skip.season.check) checkSeason(grid, ref)
     ref.m <- suppressMessages({
       climatology(ref, clim.fun, by.member, parallel, max.ncores,ncores)
     }) %>% redim()