Doc update

SantanderMetGroup · May 23, 2020 · 4352395 · 4352395
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -22,13 +22,14 @@ Imports:
     grDevices,
     data.table
 Suggests:
+    climate4R.datasets,
     loadeR.ECOMS,
     loadeR,
     knitr
 Type: Package
 Title: Visualizing climate4R data and Communicating Uncertainty in Seasonal Climate Prediction
 Version: 1.6.0
-Date: 2020-05-22
+Date: 2020-05-23
 Author: as.person(c(
     "Santander Meteorology Group <http://meteo.unican.es> [cph]",
     "María Dolores Frías <[email protected]> [aut, cre]",

diff --git a/NAMESPACE b/NAMESPACE
@@ -7,6 +7,7 @@ export(cascadePlot)
 export(climagram)
 export(densityPlot)
 export(detrend.data)
+export(draw.world.lines)
 export(map.hatching)
 export(map.lines)
 export(map.stippling)
@@ -107,7 +108,6 @@ importFrom(transformeR,checkTemporalConsistency)
 importFrom(transformeR,clim2sgdf)
 importFrom(transformeR,climatology)
 importFrom(transformeR,detrendGrid)
-importFrom(transformeR,draw.world.lines)
 importFrom(transformeR,getCoordinates)
 importFrom(transformeR,getDim)
 importFrom(transformeR,getGrid)

diff --git a/NEWS b/NEWS
@@ -49,7 +49,7 @@
 * Add boxplot option in violinPlot
 * Other minor doc updates
 
-## v1.6.0 (22 May 2020)
-* Add plotEOF (deprecated), formerly in transformeR
+## v1.6.0 (23 May 2020)
+* Add plotEOF (deprecated) and draw.world.lines utility, formerly in transformeR
 * Load example datasets from the new climate4R.datasets package
 * Other documentation and example updates
diff --git a/R/bubblePlot.R b/R/bubblePlot.R
@@ -50,7 +50,7 @@
 #' 
 #' @importFrom scales alpha
 #' @importFrom mapplots draw.pie add.pie
-#' @importFrom transformeR array3Dto2Dmat mat2Dto3Darray draw.world.lines interpGrid subsetGrid
+#' @importFrom transformeR array3Dto2Dmat mat2Dto3Darray interpGrid subsetGrid
 #' @importFrom abind abind
 #' @importFrom grDevices gray
 #' @importFrom graphics par plot mtext points legend
@@ -359,7 +359,7 @@ bubblePlot <- function(hindcast, obs, forecast=NULL, year.target=NULL, detrend=F
         }        
       } 
       # Add borders
-      draw.world.lines(lwd=1)
+      draw.world.lines(lwd = 1)
       #world(add = TRUE, interior = T)      
       #world(add = TRUE, interior = F, lwd=3)    
       par(fig = c(0, 1, 0, 1), oma = c(0, 0, 0, 0), mar = c(0, 0, 0, 0), new = TRUE)

diff --git a/R/rdas.R b/R/rdas.R
@@ -5,8 +5,7 @@
 #' @name tas.ncep
 #' @examples
 #' data(tas.ncep)
-#' require(transformeR)
-#' plotClimatology(climatology(tas.ncep), backdrop.theme = "coastline")
+#' spatialPlot(climatology(tas.ncep), backdrop.theme = "coastline", rev.colors = TRUE)
 NULL
 
 
@@ -20,8 +19,7 @@ NULL
 #' @references Saha, S. et al. 2014. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
 #' @examples \dontrun{
 #' data(tas.cfs)
-#' require(transformeR)
-#' plotClimatology(climatology(tas.cfs), backdrop.theme = "coastline")
+#' spatialPlot(climatology(tas.cfs), backdrop.theme = "coastline", rev.colors = TRUE)
 #' }
 NULL
 
@@ -37,8 +35,7 @@ NULL
 #' @references Saha, S. et al. 2014. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
 #' @examples \dontrun{
 #' data(tas.cfs.operative.2016)
-#' require(transformeR)
-#' plotClimatology(climatology(tas.cfs.operative.2016, parallel = TRUE), backdrop.theme = "coastline")
+#' spatialPlot(climatology(tas.cfs.operative.2016, parallel = TRUE), backdrop.theme = "coastline", rev.colors = TRUE)
 #' }
 NULL
 
@@ -53,8 +50,7 @@ NULL
 #' @references Saha, S. et al. 2014. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
 #' @examples \dontrun{
 #' data(tas.cfs.operative.2017)
-#' require(transformeR)
-#' plotClimatology(climatology(tas.cfs.operative.2017, parallel = TRUE), backdrop.theme = "coastline")
+#' spatialPlot(climatology(tas.cfs.operative.2017, parallel = TRUE), backdrop.theme = "coastline", rev.colors = TRUE)
 #' }
 NULL
 
@@ -66,8 +62,10 @@ NULL
 #' @name AR5regions
 #' @examples \dontrun{
 #' data(AR5regions)
+#' require(sp)
+#' require(transformeR)
 #' sp::plot(AR5regions, border = "red", axes = TRUE)
-#' transformeR:::draw.world.lines()
+#' draw.world.lines()
 #' title("AR5 World regions")
 #' }
 NULL
@@ -79,8 +77,10 @@ NULL
 #' @name PRUDENCEregions
 #' @examples \dontrun{
 #' data(PRUDENCEregions)
+#' require(sp)
+#' require(transformeR)
 #' sp::plot(PRUDENCEregions, border = "red", axes = TRUE)
-#' transformeR:::draw.world.lines()
+#' draw.world.lines()
 #' title("PRUDENCE European regions")
 #' }
 NULL
@@ -106,12 +106,12 @@ NULL
 #' 
 #' # All regions
 #' sp::plot(AR6_WGI_AtlasSynthesisRegions, border = "red", axes = TRUE)
-#' transformeR:::draw.world.lines()
+#' draw.world.lines()
 #' title("AR6 World land regions")
 #' 
 #' # A single region (use region names for subsetting)
 #' sp::plot(AR6_WGI_AtlasSynthesisRegions["Africa"], border = "red", axes = TRUE)
-#' transformeR:::draw.world.lines()
+#' draw.world.lines()
 #' title("AR6 Mediterranean region")
 #' }
 NULL
diff --git a/R/reliabilityCategories.R b/R/reliabilityCategories.R
@@ -39,8 +39,8 @@
 #' are reescaled according to parameter \code{cex.scale}.
 #' @param cex.scale numeric (default is 20). Scaling factor for points sizes in the reliability diagrams (see parameter \code{cex0}) 
 #' @param layout integer (default = c(1, n.events)). Sets the layout of panels (rows,cols)
-#' @param backdrop.theme Reference geographical lines to be added to the plot. Default is "countries" 
-#' (See \code{\link[transformeR]{plotClimatology}} for options).
+#' @param backdrop.theme Reference geographical lines to be added to the plot. Default is \code{"countries"} 
+#' (See \code{\link{spatialPlot}} for other options).
 #' @param return.diagrams Logical. Available when \code{diagrams = TRUE}. If TRUE a trellis object for plotting diagrams is returned.
 # @param nod Required if diagrams = TRUE. m*2 matrix of coordinates (m=locations, column1=latitude, column2=longitude)
 # @param xlim Required if diagrams = TRUE. Limits for maps
@@ -97,7 +97,8 @@
 #' rel <- reliabilityCategories(hindcast = tas.cfs2.int, obs = tas.ncep2,
 #'                              n.bins = 5, n.boot = 10)
 #' # Irregular grids
-#' data("VALUE_Iberia_tas")
+#' require(climate4R.datasets) 
+#' data("NCEP_Iberia_tas")
 #' data("CFS_Iberia_tas")
 #' obs <- aggregateGrid(VALUE_Iberia_tas, aggr.y = list(FUN= mean))
 #' hind <- aggregateGrid(interpGrid(NCEP_Iberia_tas, getGrid(obs)), aggr.y = list(FUN= mean))

diff --git a/R/spatialPlot.R b/R/spatialPlot.R
@@ -85,8 +85,9 @@
 #'  \code{\link{map.stippling}}, for adding a custom point layer on top of the map.
 #'  \code{\link{map.lines}}, to add lines and polygons to climatological maps
 #' Also see \code{\link[sp]{spplot}} in package \pkg{sp} for further information on plotting capabilities and options
-#' @examples
+#' @examples \donttest{
 #' require(transformeR)
+#' require(climate4R.datasets)
 #' data("CFS_Iberia_tas")
 #' # Climatology is computed:
 #' clim <- climatology(CFS_Iberia_tas, by.member = TRUE)
@@ -169,6 +170,7 @@
 #'             backdrop.theme = "countries",
 #'             color.theme = "BrBG",
 #'             rev.colors = TRUE, cex = 2.5)
+#' }
 
 
 spatialPlot <- function(grid,
@@ -258,7 +260,9 @@ spatialPlot <- function(grid,
 #' @seealso \code{\link{spatialPlot}}, to which its output is passed.
 #'  \code{\link{map.lines}}, for further map customizations.
 #' @author J. Bedia
-#' @examples
+#' @examples \donttest{
+#' require(climate4R.datasets)
+#' require(transformeR)
 #' data("CFS_Iberia_tas")
 #' p90clim <- climatology(CFS_Iberia_tas,
 #'                        by.member = FALSE,
@@ -289,6 +293,7 @@ spatialPlot <- function(grid,
 #' spatialPlot(climatology(CFS_Iberia_tas),
 #'                 backdrop.theme = "coastline",
 #'                 sp.layout = list(pts))
+#' }
 
 
 map.stippling <- function(clim, threshold = 0.05, condition = "LT", ...) {
@@ -336,7 +341,9 @@ map.stippling <- function(clim, threshold = 0.05, condition = "LT", ...) {
 #' @export
 #' @seealso \code{\link{spatialPlot}}, to which its output is passed.
 #'  \code{\link{map.stippling}}, for further map customizations.
-#' @examples 
+#' @examples \donttest{
+#' require(climate4R.datasets)
+#' require(transformeR)
 #' data("CFS_Iberia_tas")
 #' # Define a rectangular window centered on the Iberian Peninsula
 #' iberia <- map.lines(lonLim = c(-10,3.5), latLim = c(36,43))
@@ -358,7 +365,7 @@ map.stippling <- function(clim, threshold = 0.05, condition = "LT", ...) {
 #' spatialPlot(climatology(CFS_Iberia_tas, by.member = FALSE), backdrop.theme = "coastline",
 #'                 sp.layout = list(iberia, alps))
 #' 
-#' \dontrun{
+#' 
 #' # Adding a line (real data of a storm-track imported from a csv file)
 #' # Source: http://www.europeanwindstorms.org/
 #' 

diff --git a/R/temporalPlot.R b/R/temporalPlot.R
@@ -70,9 +70,12 @@
 #'@importFrom data.table rleid
 #'@importFrom transformeR gridDepth
 #'@import latticeExtra
-#' @examples
+#' @examples \donttest{
+#' require(climate4R.datasets)
+#' require(transformeR)
 #' data("CFS_Iberia_pr")
 #' data("EOBS_Iberia_pr")
+#' data("EOBS_Iberia_tas")
 #' data("VALUE_Iberia_pr")
 #' # Combine grids with members (CFS) and without members (EOBS)
 #' a <- subsetGrid(CFS_Iberia_tas, years = 1985:1992)
@@ -94,6 +97,7 @@
 #' temporalPlot("EOBS" = b1, "CFS" = a1,
 #'              cols = c("green", "deeppink"), show.na = TRUE,
 #'              xyplot.custom = list(main = "winter temperature", ylab = "Celsius"))
+#' }
 
 
 temporalPlot <- function(..., 

diff --git a/R/tercileMap.R b/R/tercileMap.R
@@ -42,11 +42,14 @@
 #'@export
 #'@importFrom grDevices colorRampPalette
 #'@importFrom transformeR aggregateGrid subsetGrid getShape redim climatology bindGrid
-#' @examples
+#' @examples \donttest{
+#' require(climate4R.datasets)
+#' data(CFS_Iberia_tas)
 #' library(transformeR)
 #' hindcast <- subsetGrid(CFS_Iberia_tas, years = 1983:2001)
 #' forecast <- subsetGrid(CFS_Iberia_tas, years = 2002)
 #' tercileMap(hindcast, forecast)
+#' }
 
 tercileMap <- function(hindcast, forecast, ...) {
       custom <- list(...)

diff --git a/R/violinPlot.R b/R/violinPlot.R
@@ -65,7 +65,8 @@
 #' @importFrom transformeR gridDepth
 #' @importFrom stats sd
 #' @import latticeExtra
-#' @examples
+#' @examples \donttest{
+#' require(climate4R.datasets)
 #' data("EOBS_Iberia_tas")
 #' data("EOBS_Iberia_pr")
 #' data("CORDEX_Iberia_pr")
@@ -122,6 +123,7 @@
 #'                                      as.table = TRUE,
 #'                                      do.out = FALSE))
 #' a + b
+#' }
 
 
 violinPlot <- function(..., 

diff --git a/data/AR5regions.rda b/data/AR5regions.rda
diff --git a/data/PRUDENCEregions.rda b/data/PRUDENCEregions.rda
diff --git a/data/regions.rda b/data/regions.rda
diff --git a/data/tas.cfs.operative.2016.rda b/data/tas.cfs.operative.2016.rda
diff --git a/data/tas.cfs.operative.2017.rda b/data/tas.cfs.operative.2017.rda
diff --git a/data/tas.cfs.rda b/data/tas.cfs.rda
diff --git a/data/tas.ncep.rda b/data/tas.ncep.rda
diff --git a/man/AR5regions.Rd b/man/AR5regions.Rd
diff --git a/man/AR6_WGI_AtlasSynthesisRegions.Rd b/man/AR6_WGI_AtlasSynthesisRegions.Rd
diff --git a/man/PRUDENCEregions.Rd b/man/PRUDENCEregions.Rd
diff --git a/man/map.lines.Rd b/man/map.lines.Rd
diff --git a/man/map.stippling.Rd b/man/map.stippling.Rd
diff --git a/man/plotEOF.Rd b/man/plotEOF.Rd
diff --git a/man/reliabilityCategories.Rd b/man/reliabilityCategories.Rd
diff --git a/man/spatialPlot.Rd b/man/spatialPlot.Rd