Merge branch 'devel'

Establish version

.gitignore

@@ -3,4 +3,5 @@
 .RData
 ignore/
 .Rbuildignore
-.*
+.*
+visualizeR.Rproj

DESCRIPTION

@@ -21,24 +21,24 @@ Suggests:
     knitr
 Type: Package
 Title: Visualizing and Communicating Uncertainty in Seasonal Climate Prediction
-Version: 0.2-0
-Date: 2016-03-06
+Version: 0.2.1
+Date: 2017-05-05
 Authors@R: as.person(c(
-    "Maria Dolores Frias <[email protected]> [ctb, cre]",
-    "Jesus Fernandez <[email protected]> [ctb]",
-    "Joaquin Bedia <[email protected]> [ctb]",
+    "Santander Meteorology Group <http://meteo.unican.es> [ctb]",
+    "Maria Dolores Frias <[email protected]> [aut, cre]",
+    "Jesus Fernandez <[email protected]> [aut]",
+    "Maialen Iturbide <[email protected]> [aut]",
+    "Joaquin Bedia <[email protected]> [aut]",
     "Max Tuni <[email protected]> [ctb]",
     "Sixto Herrera <[email protected]> [ctb]",
     "Rodrigo Manzanas <[email protected]> [ctb]",
     "Antonio Cofino <[email protected]> [ctb]",
-    "Maialen Iturbide <[email protected]> [ctb]",
     "Jose Manuel Gutierrez <[email protected]> [ctb]",
     "Andrea Taylor <[email protected]> [ctb]",
-    "Aidan Slingsby <[email protected]> [ctb]",
-    "Santander Meteorology Group <http://meteo.unican.es> [aut]"))
+    "Aidan Slingsby <[email protected]> [ctb]"))
 BugReports: https://github.com/SantanderMetGroup/visualizeR/issues
 URL: https://github.com/SantanderMetGroup/visualizeR/wiki
-Description: Implementation of various seasonal forecast verification plots.
+Description: Implementation of seasonal climate verification plots.
 License: file LICENSE
 LazyData: true
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1

NEWS

@@ -1,7 +1,5 @@
-visualizeR
-==========
+visualizeR 0.2.1
+=================
 
-* Added optional argument 'forecast' in all the visualizations (except reliabilityCategories) to show results for the forecast event  (not just for the hindcast).
-* Several improvements in the appearance of the visualizations.
-* Enhanced reliability diagrams, importing funcitonalities from lattice
-* Other minor changes and enhancements.
+* Minor bug in reliabilityCategories and spreadPlot. 
+* Other minor changes and documentation updates.

R/bubblePlot.R

@@ -1,4 +1,4 @@
-##     bubblePlot Bubble plot for visualization of forecast skill of ensemble predictions.
+##     bubblePlot Bubble plot for visualization of forecast skill of seasonal climate predictions.
 ##
 ##     Copyright (C) 2016 Santander Meteorology Group (http://www.meteo.unican.es)
 ##
@@ -15,9 +15,9 @@
 ##     You should have received a copy of the GNU General Public License
 ##     along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#' @title Bubble plot for visualization of forecast skill of ensemble predictions.
+#' @title Bubble plot for visualization of forecast skill of seasonal climate predictions.
 #' 
-#' @description Bubble plot for visualization of forecast skill of ensemble predictions. It provides a
+#' @description Bubble plot for visualization of forecast skill of seasonal climate predictions. It provides a
 #'  spatially-explicit representation of the skill, resolution and reliability of a probabilistic predictive 
 #'  system in a single map. 
 #'  This function is prepared to plot the data sets loaded from the ECOMS User Data Gateway (ECOMS-UDG). See 
@@ -77,16 +77,42 @@
 #' 
 #' @note The computation of climatological terciles requires a representative period to obtain meaningful results.
 #' 
+#' @examples \dontrun{
+#' data(tas.cfs)
+#' data(tas.cfs.operative.2016)
+#' data(tas.ncep)
+#' require(transformeR)
+#' # Select spatial domain
+#' tas.ncep2 <- subsetGrid(tas.ncep, lonLim = c(-80, -35), latLim = c(-12, 12))
+#' tas.cfs2 <- subsetGrid(tas.cfs, lonLim = c(-80, -35), latLim = c(-12, 12))
+#' tas.cfs.operative2.2016 <- subsetGrid(tas.cfs.operative.2016, 
+#'                            lonLim = c(-80, -35), latLim = c(-12, 12))
+#' # Interpolate
+#' tas.ncep2.int <- interpGrid(tas.ncep2, getGrid(tas.cfs2))
+#' # Bubble plot. Only colour of the bubble is plotted indicating the most likely tercile 
+#' bubblePlot(hindcast = tas.cfs2, obs = tas.ncep2.int, forecast = tas.cfs.operative2.2016,
+#'            bubble.size = 1.5, size.as.probability = FALSE, score = FALSE)
+#' # Bubble plot. Added size of the bubble indicating the probability of the most likely tercile 
+#' bubblePlot(hindcast = tas.cfs2, obs = tas.ncep2.int, forecast = tas.cfs.operative2.2016,
+#'            bubble.size = 1.5, score = FALSE)
+#' # Bubble plot. Added transparency of the bubble indicating the ROC skill score (ROCSS)
+#' bubblePlot(hindcast = tas.cfs2, obs = tas.ncep2.int, forecast = tas.cfs.operative2.2016,
+#'            bubble.size = 1.5)
+#' # 3-piece pie chart.
+#' bubblePlot(hindcast = tas.cfs2, obs = tas.ncep2.int, forecast = tas.cfs.operative2.2016,
+#'            bubble.size = 1, piechart = TRUE)
+#' } 
+#' 
 #' @author M.D. Frias \email{mariadolores.frias@@unican.es} and J. Fernandez based on the original diagram 
-#'  conceived by Slingsby et al 2009.
+#'  conceived by Slingsby et al (2009).
 #' 
 #' @family VisualizeR
 #' 
 #' @references
 #'  Jolliffe, I. T. and Stephenson, D. B. 2003. Forecast Verification: A Practitioner's Guide in Atmospheric 
 #'  Science, Wiley, NY.
 #'  
-#'  Slingsby A., Lowe R., Dykes J., Stephenson D. B., Wood J., Jupp T. E. 2009. A pilot study for the collaborative 
+#'  Slingsby A., Lowe R., Dykes J., Stephenson D. B., Wood J. and Jupp T. E. 2009. A pilot study for the collaborative 
 #'  development of new ways of visualising seasonal climate forecasts. Proc. 17th Annu. Conf. of GIS Research UK, 
 #'  Durham, UK, 1-3 April 2009.
 
@@ -370,7 +396,11 @@ bubblePlot <- function(hindcast, obs, forecast=NULL, year.target=NULL, detrend=F
           } else{
             legtext <- c("Below", "Normal", "Above")     
           }
-          legend('bottomleft', legend=legtext, pch=c(19, 19, 19), col=c(t.colors), cex=0.7, horiz=T, bty="n", xjust=0)        
+          xcoords <- c(0, 0.55, 0.95)
+          secondvector <- (1:length(legtext))-1
+          textwidths <- xcoords/secondvector 
+          textwidths[1] <- 0        
+          legend('bottomleft', legend=legtext, pch=c(19, 19, 19), col=c(t.colors), cex=0.7, horiz=T, bty="n", text.width=textwidths, xjust=0)        
         }  
       }
       par(opar)