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SantanderMetGroup · Feb 1, 2017 · 0b9f4c3 · 0b9f4c3
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+ignore
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,6 @@
 .Rproj.user
 .Rhistory
 .RData
+ignore/
+.Rbuildignore
+.*
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -20,7 +20,7 @@ Suggests:
 Type: Package
 Title: R Package with visualization tools for forecast verification
 Version: 0.1-0
-Date: 2016-11-30
+Date: 2016-02-01
 Authors@R: as.person(c(
     "Maria Dolores Frias <[email protected]> [ctb, cre]",
     "Jesus Fernandez <[email protected]> [ctb]",
@@ -36,9 +36,7 @@ Authors@R: as.person(c(
     "Santander Meteorology Group <http://meteo.unican.es> [aut]"))
 BugReports: https://github.com/SantanderMetGroup/visualizeR/issues
 URL: https://github.com/SantanderMetGroup/visualizeR/wiki
-Description: Load climate data (forecasts and observations) into R and performs
-    different type of verification plots. The package is
-    conceived for dealing with forecast (multi-member) data.
+Description: Implementation of various seasonal forecast verification plots. 
 License: file LICENSE
 LazyData: true
 RoxygenNote: 5.0.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -53,9 +53,11 @@ importFrom(stats,lm)
 importFrom(stats,quantile)
 importFrom(transformeR,array3Dto2Dmat)
 importFrom(transformeR,draw.world.lines)
+importFrom(transformeR,getCoordinates)
 importFrom(transformeR,getDim)
 importFrom(transformeR,getGrid)
 importFrom(transformeR,getYearsAsINDEX)
+importFrom(transformeR,interpGrid)
 importFrom(transformeR,makeMultiGrid)
 importFrom(transformeR,mat2Dto3Darray)
 importFrom(transformeR,redim)

diff --git a/NEWS b/NEWS
@@ -1,6 +1,6 @@
 visualizeR
 ==========
 
-* New built-in datasets: DJF global mean sea-level pressure, temperature and total precipitation from NCEP/NCAR reanalysis and NCEP-CFSv2 hindcast. Global operative CFSv2 seasonal forecasts for global temperature and precipitation (DJF 2016 and 2017)
+* New built-in datasets: DJF global mean temperature from NCEP/NCAR reanalysis, NCEP-CFSv2 hindcast and CFSv2 Operative seasonal forecasts for DJF 2016 and 2017.
 * New function for reliability diagram, implementing the approach in Weisheimer and Palmer 2014 (DOI: 10.1098/rsif.2013.1162) 
 * Other minor bug fixes and enhancements
diff --git a/R/auxiliaryFun.R b/R/auxiliaryFun.R
@@ -75,6 +75,8 @@ tercileColor <- function(){
 
 # Check xyCoords from two datasets
 #' @keywords internal
+#' @importFrom transformeR getCoordinates
+#' 
 checkCoords <- function (data1, data2){
   v<-FALSE
   if (is.null(data1) | is.null(data2)) v <-TRUE

diff --git a/R/bubblePlot.R b/R/bubblePlot.R
@@ -48,7 +48,7 @@
 #' 
 #' @importFrom scales alpha
 #' @importFrom mapplots draw.pie add.pie
-#' @importFrom transformeR array3Dto2Dmat mat2Dto3Darray draw.world.lines
+#' @importFrom transformeR array3Dto2Dmat mat2Dto3Darray draw.world.lines interpGrid
 #' @importFrom abind abind
 #' @importFrom grDevices gray
 #' @importFrom graphics par plot mtext points legend

diff --git a/R/rdas.R b/R/rdas.R
@@ -1,31 +1,3 @@
-#' @title NCEP/NCAR reanalysis DJF mean sea-level pressure for the entire globe
-#' @description NCEP/NCAR reanalysis DJF mean sea-level pressure for the entire globe (1949-2010). Data are annually aggregated.
-#' @format A grid
-#' @source Dowloaded from the ECOMS User Data Gateway \url{http://www.meteo.unican.es/ecoms-udg}
-#' @name psl.ncep
-#' @examples
-#' data(psl.ncep)
-#' require(transformeR)
-#' plotClimatology(climatology(psl.ncep), backdrop.theme = "coastline")
-NULL
-
-
-#' @title NCEP CFSv2 hindcast of DJF mean sea-level pressure for the entire globe.
-#' @description NCEP CFSv2 hindcast for DJF mean sea-level pressure for the entire globe (1983-2010). Data are annually aggregated.
-#' Ensemble of 24 members, corresponding to the lead month 1 predictions (November initializations)
-#' @format A grid
-#' @description For further detail on ensemble member definition, see \url{http://www.meteo.unican.es/ecoms-udg/dataserver/datasets/CFSv2}
-#' @source Dowloaded from the ECOMS User Data Gateway \url{http://www.meteo.unican.es/ecoms-udg}
-#' @name psl.cfs
-#' @references Saha, S. et al. 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
-#' @examples \dontrun{
-#' data(psl.cfs)
-#' require(transformeR)
-#' plotClimatology(climatology(psl.cfs), backdrop.theme = "coastline")
-#' }
-NULL
-
-
 #' @title NCEP/NCAR reanalysis DJF mean temperature for the entire globe
 #' @description NCEP/NCAR reanalysis DJF mean temperature for the entire globe (1949-2010). Data are annually aggregated.
 #' @format A grid
@@ -54,68 +26,6 @@ NULL
 NULL
 
 
-#' @title NCEP/NCAR reanalysis DJF total precipitation amount for the entire globe.
-#' @description NCEP/NCAR reanalysis DJF total precipitation amount for the entire globe (1949-2010). Data are annually aggregated.
-#' @format A grid
-#' @source Dowloaded from the ECOMS User Data Gateway \url{http://www.meteo.unican.es/ecoms-udg}
-#' @name tp.ncep
-#' @examples
-#' data(tp.ncep)
-#' require(transformeR)
-#' plotClimatology(climatology(tp.ncep), backdrop.theme = "coastline")
-NULL
-
-
-#' @title NCEP CFSv2 hindcast of DJF total precipitation amount for the entire globe.
-#' @description NCEP CFSv2 hindcast of DJF total precipitation amount for the entire globe (1983-2010). Data are annually aggregated.
-#' Ensemble of 24 members, corresponding to the lead month 1 predictions (November initializations)
-#' @format A grid
-#' @description For further detail on ensemble member definition, see \url{http://www.meteo.unican.es/ecoms-udg/dataserver/datasets/CFSv2}
-#' @source Dowloaded from the ECOMS User Data Gateway \url{http://www.meteo.unican.es/ecoms-udg}
-#' @name tp.cfs
-#' @references Saha, S. et al. 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
-#' @examples \dontrun{
-#' data(tp.cfs)
-#' require(transformeR)
-#' plotClimatology(climatology(tp.cfs), backdrop.theme = "coastline")
-#' }
-NULL
-
-
-#' @title CFSv2 operative seasonal forecast of global DJF total precipitation amount (2016)
-#' @description CFSv2 operative seasonal forecast of DJF total precipitation amount for the entire globe of year 2016
-#'  (i.e. December 2015, Januery-February 2016). Data are annually aggregated. Ensemble of 24 members,
-#'   corresponding to the lead month 1 predictions (November 2015 initializations).
-#' @format A grid
-#' @description For further detail on ensemble member definition, see \url{http://www.meteo.unican.es/ecoms-udg/dataserver/datasets/CFSv2}
-#' @source Dowloaded from the ECOMS User Data Gateway \url{http://www.meteo.unican.es/ecoms-udg}
-#' @name tp.cfs.operative.2016
-#' @references Saha, S. et al. 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
-#' @examples \dontrun{
-#' data(tp.cfs.operative.2016)
-#' require(transformeR)
-#' plotClimatology(climatology(tp.cfs.operative.2016, parallel = TRUE), backdrop.theme = "coastline")
-#' }
-NULL
-
-#' @title CFSv2 operative seasonal forecast of global DJF total precipitation amount (2017)
-#' @description CFSv2 operative seasonal forecast of DJF total precipitation amount for the entire globe of year 2017
-#'  (i.e. December 2016, Januery-February 2017). Data are annually aggregated. Ensemble of 24 members,
-#'   corresponding to the lead month 1 predictions (November 2016 initializations).
-#' @format A grid
-#' @description For further detail on ensemble member definition, see \url{http://www.meteo.unican.es/ecoms-udg/dataserver/datasets/CFSv2}
-#' @source Dowloaded from the ECOMS User Data Gateway \url{http://www.meteo.unican.es/ecoms-udg}
-#' @name tp.cfs.operative.2017
-#' @references Saha, S. et al. 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
-#' @examples \dontrun{
-#' data(tp.cfs.operative.2017)
-#' require(transformeR)
-#' plotClimatology(climatology(tp.cfs.operative.2017, parallel = TRUE), backdrop.theme = "coastline")
-#' }
-NULL
-
-
-
 #' @title CFSv2 operative seasonal forecast of global DJF mean temperature (2016)
 #' @description CFSv2 operative seasonal forecast of DJF mean temperature for the entire globe of year 2016
 #'  (i.e. December 2015, Januery-February 2016). Data are annually aggregated. Ensemble of 24 members,
@@ -149,24 +59,28 @@ NULL
 NULL
 
 #' @title AR5 regions from the IPCC 5th Assessment Report.
-#' @description SpatialPolygons object of the geographical regions used in the IPCC 5th Assessment Report.
-#' @format A SpatialPolygons object
+#' @description Spatial Polygons of the geographical regions used in the IPCC 5th Assessment Report.
+#' @format A \code{\link[sp]{SpatialPolygons-class}} object
 #' @description For further detail, see \url{http://www.ipcc-data.org/guidelines/pages/ar5_regions.html}
 #' @source Shapefile imported with function \code{\link[rgdal]{readOGR}} (\url{http://www.ipcc-data.org/guidelines/pages/ar5_regions.html})
 #' @name AR5regions
 #' @examples \dontrun{
 #' data(AR5regions)
-#' plot(AR5regions)
+#' sp::plot(AR5regions, border = "red", axes = TRUE)
+#' transformeR:::draw.world.lines()
+#' title("AR5 World regions")
 #' }
 NULL
 
 #' @title PRUDENCE regions.
-#' @description SpatialPolygons object of the geographical regions used in the PRUDENCE project.
-#' @format A SpatialPolygons object
+#' @description Spatial Polygons of the geographical regions used in the PRUDENCE project.
+#' @format A \code{\link[sp]{SpatialPolygons-class}} object
 #' @description For further detail, see \url{http://ensemblesrt3.dmi.dk/quicklook/regions.html}
 #' @name PRUDENCEregions
 #' @examples \dontrun{
 #' data(PRUDENCEregions)
-#' plot(PRUDENCEregions)
+#' sp::plot(PRUDENCEregions, border = "red", axes = TRUE)
+#' transformeR:::draw.world.lines()
+#' title("PRUDENCE European regions")
 #' }
-NULL
+NULL
diff --git a/man/AR5regions.Rd b/man/AR5regions.Rd
diff --git a/man/PRUDENCEregions.Rd b/man/PRUDENCEregions.Rd
diff --git a/man/psl.cfs.Rd b/man/psl.cfs.Rd
diff --git a/man/psl.ncep.Rd b/man/psl.ncep.Rd
diff --git a/man/tp.cfs.Rd b/man/tp.cfs.Rd
diff --git a/man/tp.cfs.operative.2016.Rd b/man/tp.cfs.operative.2016.Rd
diff --git a/man/tp.cfs.operative.2017.Rd b/man/tp.cfs.operative.2017.Rd