Several changes for successful R CMD check

SantanderMetGroup · Aug 22, 2014 · 90906d1 · 90906d1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,17 +1,19 @@
 Package: downscaleR
 Depends:
+    rJava,
     downscaleR.java,
+    maps,
+    R(>= 3.0.0)
+Imports:
     utils,
     RCurl,
-    rJava,
     abind,
     fields,
-    MASS,
-    R(>= 3.0.0)
+    MASS
 Type: Package
 Title: R package for climate data analysis and downscaling
 Version: 0.2-2
-Date: 20-Aug-2014
+Date: 22-Aug-2014
 Author: Santander Meteorology Group <http://www.meteo.unican.es>
 Maintainer: Joaquin Bedia <[email protected]>
 BugReports: https://github.com/SantanderMetGroup/downscaleR/issues

diff --git a/NAMESPACE b/NAMESPACE
@@ -14,17 +14,14 @@ export(getGrid)
 export(getLatLonDomain)
 export(getTimeDomain)
 export(hurs2huss)
-export(iberia_ncep_hus850)
-export(iberia_ncep_psl)
-export(iberia_ncep_ta850)
 export(interpGridData)
 export(isimip)
 export(loadGridData)
 export(loadMultiField)
 export(loadStationData)
 export(login_SMG)
 export(makeAggregatedDataset)
-export(makeMultifield)
+export(makeMultiField)
 export(makeSubset)
 export(mat2Dto3Darray)
 export(mslp2ps)
@@ -33,12 +30,10 @@ export(plotMeanField)
 export(prinComp)
 export(revArrayLatDim)
 export(scanVarDimensions)
-export(tasmax_forecast)
-export(tasmin_forecast)
 export(tdps2hurs)
 export(timeBounds)
 export(toDD)
-export(tp_forecast)
+import(maps)
 import(rJava)
 importFrom(MASS,fitdistr)
 importFrom(RCurl,getURL)

diff --git a/R/iberia_ncep_hus850.R b/R/iberia_ncep_hus850.R
@@ -5,8 +5,7 @@
 #' @format A field
 #' @source \url{http://www.meteo.unican.es/ecoms-udg}
 #' @name iberia_ncep_hus850
-#' @export
-#' @seealso \code{\link{makeMultifield}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+#' @seealso \code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 #' @examples
 #' data(iberia_ncep_hus850)
 #' plotMeanField(iberia_ncep_hus850)

diff --git a/R/iberia_ncep_psl.R b/R/iberia_ncep_psl.R
@@ -6,8 +6,7 @@
 #' @format A field
 #' @source \url{http://www.meteo.unican.es/ecoms-udg}
 #' @name iberia_ncep_psl
-#' @export
-#' @seealso \code{\link{makeMultifield}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+#' @seealso \code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 #' @examples
 #' data(iberia_ncep_psl)
 #' plotMeanField(iberia_ncep_psl)

diff --git a/R/iberia_ncep_ta850.R b/R/iberia_ncep_ta850.R
@@ -5,8 +5,7 @@
 #' @format A field
 #' @source \url{http://www.meteo.unican.es/ecoms-udg}
 #' @name iberia_ncep_ta850
-#' @export
-#' @seealso \code{\link{makeMultifield}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+#' @seealso \code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 #' @examples
 #' data(iberia_ncep_ta850)
 #' plotMeanField(iberia_ncep_ta850)

diff --git a/R/isimip.R b/R/isimip.R
@@ -215,7 +215,7 @@ isimip <- function (obs, pred, sim, pr.threshold = 1) {
       if (any(grepl(obs$Variable$varName,c("pr","tp","precipitation","precip")))){
             threshold<-pr.threshold
             if (length(threshold)==1){
-                  threshold<-array(dat = threshold, dim = 3)
+                  threshold<-array(data = threshold, dim = 3)
             }
             # First Step: Monthly Correction
             dimAux<-dimPred

diff --git a/R/plotMeanField.R b/R/plotMeanField.R
@@ -3,8 +3,8 @@
 #' @description Plot the spatial mean of a gridded variable, or variables in the case of multi-fields.
 #' 
 #' @importFrom fields image.plot
+#' @import maps 
 #' @importFrom fields world
-#' 
 #' @param gridData A grid dataset
 #' @param multi.member Should members be plotted sepparately (TRUE), or just a plot
 #'  of the multi-member mean (FALSE, default)?. Ignored if the dataset has no members.

diff --git a/R/prinComp.R b/R/prinComp.R
@@ -111,7 +111,7 @@
 #' # We interpolate using an identical grid than the previous example:
 #' multimember2 <- interpGridData(tasmin_forecast, new.grid = getGrid(multimember))
 #' # Now the multimember multifield is constructed
-#' mm.multifield <- mm2mm.mf(list(multimember, multimember2))
+#' mm.multifield <- makeMultiField(list(multimember, multimember2))
 #' pca.mm.mf <- prinComp(mm.multifield, n.eofs = 10)
 #' # Now there is a "COMBINED" element at the end of the output list
 #' str(pca.mm.mf)

diff --git a/R/tasmax_forecast.R b/R/tasmax_forecast.R
@@ -7,8 +7,7 @@
 #' @references 
 #' Saha, S. \emph{et al.}, 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
 #' @name tasmax_forecast
-#' @export
-#' @seealso \code{\link{mm2mm.mf}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+#' @seealso \code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 #' @examples
 #' data(tasmax_forecast)
 #' plotMeanField(tasmax_forecast, multi.member = TRUE)

diff --git a/R/tasmin_forecast.R b/R/tasmin_forecast.R
@@ -8,8 +8,7 @@
 #' Saha, S. \emph{et al.}, 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
 
 #' @name tasmin_forecast
-#' @export
-#' @seealso \code{\link{mm2mm.mf}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+#' @seealso \code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 #' @examples
 #' data(tasmin_forecast)
 #' plotMeanField(tasmin_forecast, multi.member = TRUE)

diff --git a/R/tp_forecast.R b/R/tp_forecast.R
@@ -8,8 +8,7 @@
 #' Saha, S. \emph{et al.}, 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
 
 #' @name tp_forecast
-#' @export
-#' @seealso \code{\link{mm2mm.mf}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+#' @seealso \code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 #' @examples
 #' data(tp_forecast)
 #' plotMeanField(tp_forecast, multi.member = TRUE)

diff --git a/data/iberia_ncep_hus850.Rda b/data/iberia_ncep_hus850.Rda
diff --git a/data/iberia_ncep_hus850.rda b/data/iberia_ncep_hus850.rda
diff --git a/data/iberia_ncep_psl.Rda b/data/iberia_ncep_psl.Rda
diff --git a/data/iberia_ncep_psl.rda b/data/iberia_ncep_psl.rda
diff --git a/data/iberia_ncep_ta850.Rda b/data/iberia_ncep_ta850.Rda
diff --git a/data/iberia_ncep_ta850.rda b/data/iberia_ncep_ta850.rda
diff --git a/data/tasmax_forecast.Rda b/data/tasmax_forecast.Rda
diff --git a/data/tasmax_forecast.rda b/data/tasmax_forecast.rda
diff --git a/data/tasmin_forecast.Rda b/data/tasmin_forecast.Rda
diff --git a/data/tasmin_forecast.rda b/data/tasmin_forecast.rda
diff --git a/data/tp_forecast.Rda b/data/tp_forecast.Rda
diff --git a/data/tp_forecast.rda b/data/tp_forecast.rda
diff --git a/man/getGrid.Rd b/man/getGrid.Rd
@@ -26,7 +26,6 @@ S. Herrera and J. Bedia \email{[email protected]}
 }
 \seealso{
 Other loading.grid: \code{\link{interpGridData}};
-  \code{\link{loadGridData}}; \code{\link{loadMultiField}};
-  \code{\link{plotEOF}}
+  \code{\link{loadGridData}}; \code{\link{loadMultiField}}
 }
 
diff --git a/man/iberia_ncep_hus850.Rd b/man/iberia_ncep_hus850.Rd
@@ -14,6 +14,6 @@ data(iberia_ncep_hus850)
 plotMeanField(iberia_ncep_hus850)
 }
 \seealso{
-\code{\link{makeMultifield}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+\code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 }
 
diff --git a/man/iberia_ncep_psl.Rd b/man/iberia_ncep_psl.Rd
@@ -15,6 +15,6 @@ data(iberia_ncep_psl)
 plotMeanField(iberia_ncep_psl)
 }
 \seealso{
-\code{\link{makeMultifield}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+\code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 }
 
diff --git a/man/iberia_ncep_ta850.Rd b/man/iberia_ncep_ta850.Rd
@@ -14,6 +14,6 @@ data(iberia_ncep_ta850)
 plotMeanField(iberia_ncep_ta850)
 }
 \seealso{
-\code{\link{makeMultifield}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+\code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 }
 
diff --git a/man/interpGridData.Rd b/man/interpGridData.Rd
@@ -64,7 +64,6 @@ J. Bedia \email{[email protected]} and S. Herrera
 }
 \seealso{
 Other loading.grid: \code{\link{getGrid}};
-  \code{\link{loadGridData}}; \code{\link{loadMultiField}};
-  \code{\link{plotEOF}}
+  \code{\link{loadGridData}}; \code{\link{loadMultiField}}
 }
 
diff --git a/man/loadGridData.Rd b/man/loadGridData.Rd
@@ -131,6 +131,6 @@ Other loading: \code{\link{dataInventory}};
 
 Other loading.grid: \code{\link{getGrid}};
   \code{\link{interpGridData}};
-  \code{\link{loadMultiField}}; \code{\link{plotEOF}}
+  \code{\link{loadMultiField}}
 }
 
diff --git a/man/loadMultiField.Rd b/man/loadMultiField.Rd
@@ -96,9 +96,6 @@ Other loading: \code{\link{dataInventory}};
   \code{\link{makeAggregatedDataset}}
 
 Other loading.grid: \code{\link{getGrid}};
-  \code{\link{interpGridData}}; \code{\link{loadGridData}};
-  \code{\link{plotEOF}}
-
-Other multifield: \code{\link{plotEOF}}
+  \code{\link{interpGridData}}; \code{\link{loadGridData}}
 }
 
diff --git a/man/makeMultifield.Rd → man/makeMultiField.Rd b/man/makeMultifield.Rd → man/makeMultiField.Rd
@@ -1,9 +1,9 @@
 % Generated by roxygen2 (4.0.1): do not edit by hand
-\name{makeMultifield}
-\alias{makeMultifield}
+\name{makeMultiField}
+\alias{makeMultiField}
 \title{Constructor of a multifield from various fields, supporting multimember fields.}
 \usage{
-makeMultifield(field.list)
+makeMultiField(field.list)
 }
 \arguments{
 \item{field.list}{A list containing the different input fields, either multimember or not.}
@@ -48,7 +48,7 @@ range(iberia_ncep_ta850$Dates$end) # start and end are identical (instantaneous)
 # sea-level pressure
 range(iberia_ncep_psl$Dates$start)
 range(iberia_ncep_psl$Dates$end) # start and end differ in 24 h (daily mean)
-mf <- makeMultifield(list(iberia_ncep_hus850, iberia_ncep_psl, iberia_ncep_ta850))
+mf <- makeMultiField(list(iberia_ncep_hus850, iberia_ncep_psl, iberia_ncep_ta850))
 # The new object inherits the global attributes from the first field, as it is assumed
 # that all input fields come from the same data source:
 attributes(mf)
@@ -61,7 +61,7 @@ plotMeanField(mf)
 data(tasmax_forecast)
 data(tasmin_forecast)
 data(tp_forecast)
-mm.mf <- makeMultifield(field.list = list(tasmax_forecast, tasmin_forecast, tp_forecast))
+mm.mf <- makeMultiField(field.list = list(tasmax_forecast, tasmin_forecast, tp_forecast))
 # 'plotMeanField' can just handle the multi-member mean for each variable in this case:
 plotMeanField(mm.mf)
 }
@@ -70,7 +70,7 @@ J. bedia \email{[email protected]}
 }
 \seealso{
 \code{\link{loadGridData}} and \code{\link[ecomsUDG.Raccess]{loadECOMS}} for loading fields (the latter also for loading
-multimember fields), \code{\link{loadMultifield}}, which directly loads a multifield. \code{\link{interpGridData}} and \code{\link{getGrid}}
+multimember fields), \code{\link{loadMultiField}}, which directly loads a multifield. \code{\link{interpGridData}} and \code{\link{getGrid}}
 for spatial consistency of input fields.
 }
 
diff --git a/man/plotEOF.Rd b/man/plotEOF.Rd
@@ -3,7 +3,7 @@
 \alias{plotEOF}
 \title{Plot an arbitrary number of EOFs}
 \usage{
-plotEOF(prinCompObj, var = NULL, n.eofs = NULL)
+plotEOF(prinCompObj, var = NULL, member = 1, n.eofs = NULL)
 }
 \arguments{
 \item{prinCompObj}{A PCA object as returned by \code{\link{prinComp}}}
@@ -14,31 +14,31 @@ been applied to 1 single field, this argument can be omitted.}
 \item{n.eofs}{Number of EOFs to be displayed. Default to NULL, indicating that all computed EOFS
 will be represented}
 
-\item{member}{Default to NULL, indicating that the multimember mean will be represented. Otherwise,
-this is an integer indicating the position of the member whose EOFs are to be displayed}
+\item{member}{An integer indicating the position of the member whose EOFs are to be displayed. Default 1,
+corresponding to the first member. Ignored for non multimember fields.}
 }
 \value{
 A plot with as many panels as EOFs requested, in the original units of the variable
 #
 }
 \description{
 Plots an arbitrary number of EOFs. Useful to have a quick overview of the main spatial modes
- of a field.
+ of a (possibly multimember) field.
 }
 \examples{
 \dontrun{
 # Winter temperature at 850 mb isobaric surface pressure level is loaded (period 1981--2010):
-ncep <- file.path(find.package("downscaleR"), "datasets/reanalysis/Iberia_NCEP/Iberia_NCEP.ncml")
-field <- loadGridData(ncep, var = "ta@85000", season = c(12,1,2), years = 1981:2010)
+data(iberia_ncep_ta850)
 # PCA analysis, retaining the PCs that explain 95\\\% of the total variance:
-pca <- prinComp(field, v.exp = .95)
+pca <- prinComp(iberia_ncep_ta850, v.exp = .95)
 # Plot of all EOFs
 plotEOF(pca)
 # Plot the first 4 EOFs:
 plotEOF(pca, n.eofs = 4)
 
 # Example with PCA analysis of a multifield (multiple variables)
 load geopotential heigth at 500 mb, temperature at 1000 mb and sea-level pressure
+ncep <- file.path(find.package("downscaleR"), "datasets/reanalysis/Iberia_NCEP/Iberia_NCEP.ncml")
 multifield <- loadMultiField(ncep, vars = c("z@50000", "ta@100000", "psl"), season = c(12,1,2), years = 1981:2010)
 # PCA analysis, retaining the first 9 PCs of each variable:
 pca2 <- prinComp(multifield, n.eofs = 9)
@@ -53,10 +53,6 @@ plotEOF(pca2, "psl", n.eofs = 2)
 J. Bedia \email{joaquin.bedia@gmail.com}
 }
 \seealso{
-Other loading.grid: \code{\link{getGrid}};
-  \code{\link{interpGridData}}; \code{\link{loadGridData}};
-  \code{\link{loadMultiField}}
-
-Other multifield: \code{\link{loadMultiField}}
+\code{\link{prinComp}}
 }
 
diff --git a/man/prinComp.Rd b/man/prinComp.Rd
@@ -114,7 +114,7 @@ data(tasmin_forecast)
 # We interpolate using an identical grid than the previous example:
 multimember2 <- interpGridData(tasmin_forecast, new.grid = getGrid(multimember))
 # Now the multimember multifield is constructed
-mm.multifield <- mm2mm.mf(list(multimember, multimember2))
+mm.multifield <- makeMultiField(list(multimember, multimember2))
 pca.mm.mf <- prinComp(mm.multifield, n.eofs = 10)
 # Now there is a "COMBINED" element at the end of the output list
 str(pca.mm.mf)

diff --git a/man/tasmax_forecast.Rd b/man/tasmax_forecast.Rd
@@ -17,6 +17,6 @@ plotMeanField(tasmax_forecast, multi.member = TRUE)
 Saha, S. \emph{et al.}, 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
 }
 \seealso{
-\code{\link{mm2mm.mf}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+\code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 }
 
diff --git a/man/tasmin_forecast.Rd b/man/tasmin_forecast.Rd
@@ -17,6 +17,6 @@ plotMeanField(tasmin_forecast, multi.member = TRUE)
 Saha, S. \emph{et al.}, 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
 }
 \seealso{
-\code{\link{mm2mm.mf}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+\code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 }
 
diff --git a/man/tp_forecast.Rd b/man/tp_forecast.Rd
@@ -17,6 +17,6 @@ plotMeanField(tp_forecast, multi.member = TRUE)
 Saha, S. \emph{et al.}, 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
 }
 \seealso{
-\code{\link{mm2mm.mf}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
+\code{\link{makeMultiField}}, \code{\link[ecomsUDG.Raccess]{loadECOMS}}
 }