Additions and fixes for new version release

SantanderMetGroup · Apr 1, 2015 · 49d465d · 49d465d
1 parent aa61c97
commit 49d465d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,19 +11,21 @@ Imports:
     fields,
     MASS,
     verification,
-    scales
+    scales,
+    ncdf4
 Suggests:
     ecomsUDG.Raccess,
     R.VALUE
 Type: Package
 Title: Climate data manipulation and statistical downscaling
-Version: 0.5-2
-Date: 22-Jan-2015
+Version: 0.6-0
+Date: 01-Apr-2015
 Authors@R: as.person(c(
     "Joaquin Bedia <[email protected]> [ctb, cre]",
     "Sixto Herrera <[email protected]> [ctb]",
     "Maria Dolores Frias <[email protected]> [ctb]",
     "Jesus Fernandez <[email protected]> [ctb]",
+    "Wietse Franssen <[email protected]> [ctb]",
     "Max Tuni <[email protected]> [ctb]",
     "Antonio Cofino <[email protected]> [ctb]",
     "Santander Meteorology Group <http://meteo.unican.es> [aut]"))

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.0.2): do not edit by hand
+# Generated by roxygen2 (4.1.0): do not edit by hand
 
 export(aggr6hToDailyMean)
 export(analogs)
@@ -19,6 +19,7 @@ export(getLatLonDomain)
 export(getSeason)
 export(getTimeDomain)
 export(getYearsAsINDEX)
+export(grid2NetCDF)
 export(hurs2huss)
 export(interpGridData)
 export(isimip)
@@ -55,6 +56,12 @@ importFrom(fields,image.plot)
 importFrom(fields,interp.surface.grid)
 importFrom(fields,rdist)
 importFrom(fields,world)
+importFrom(ncdf4,nc_close)
+importFrom(ncdf4,nc_create)
+importFrom(ncdf4,ncatt_put)
+importFrom(ncdf4,ncdim_def)
+importFrom(ncdf4,ncvar_def)
+importFrom(ncdf4,ncvar_put)
 importFrom(scales,alpha)
 importFrom(utils,packageDescription)
 importFrom(verification,roc.area)
diff --git a/NEWS b/NEWS
@@ -1,6 +1,6 @@
-downscaleR 0.5-2
+downscaleR 0.6-0
 ================
 
-* New features for bias correction:
-   * New options for multimember corrections
-   * New moving-window option for reference period definition
+* Several improvements in bias correction methods
+* New netCDF-4 export feature
+* Minor bug fixes
diff --git a/R/grid2Netcdf.R b/R/grid2Netcdf.R
@@ -1,7 +1,12 @@
 #' @title Write NetCDF
 #' @description Export downscaleR object to NetCDF
 #' 
-#' @import ncdf4 
+#' @importFrom ncdf4 ncdim_def 
+#' @importFrom ncdf4 ncvar_def 
+#' @importFrom ncdf4 nc_create 
+#' @importFrom ncdf4 ncatt_put 
+#' @importFrom ncdf4 ncvar_put
+#' @importFrom ncdf4 nc_close
 #' 
 #' @param data A grid data object coming from \code{\link{loadGridData}} or \code{\link{interpGridData}} 
 #'  or the function \code{\link[ecomsUDG.Raccess]{loadECOMS}} of package \pkg{ecomsUDG.Raccess}. 
@@ -14,8 +19,7 @@
 #' @param shuffle Turns on (if TRUE) or off (if FALSE, the default) the shuffle filter. According to netcdf docs, turning the shuffle filter on can improve compression for integer variables. Turning the shuffle filter on forces the created file to be in netcdf version 4 format, which will not be compatible with older software that only reads netcdf version 3 files.
 #'  
 #' @return A NetCDF-4 file with the variable and attributes defined in the inputs.
-#'  
-#' @family 
+#' 
 #' 
 #' @references
 #' 
@@ -47,64 +51,64 @@
 #' grid2NetCDF(prd.bc, NetCDFOutFile = fileName, missval = 1e20, prec = "float", globalAttributes = globalAttributes, varAttributes = varAttributes)
 #' }
 
-grid2NetCDF <- function(data, NetCDFOutFile = "out.nc4", missval = 1e20, globalAttributes = NULL, varAttributes = NULL, prec = "float", add = FALSE, compression=4, shuffle = TRUE) {
-  data(vocabulary)
-  ntime<-length(data$Dates$start)
-  tmpStdName<-as.character(vocabulary$standard_name[pmatch(vocabulary$identifier,data$Variable$varName, nomatch=0) > 0])
-  tmpUnits<-as.character(vocabulary$units[pmatch(vocabulary$identifier,data$Variable$varName, nomatch=0) > 0])
-  time.index <- grep("^time$", attr(data$Data, "dimensions"))
-  lon.index <- grep("^lon$", attr(data$Data, "dimensions"))
-  lat.index <- grep("^lat$", attr(data$Data, "dimensions"))
-  member.index <- grep("^member$", attr(data$Data, "dimensions"))
-  datesList <- as.POSIXct(data$Dates$start, tz="GMT", format="%Y-%m-%d %H:%M:%S")
-  times <- (as.double(datesList)-as.double(datesList[1]))/86400
-  dimtime <- ncdim_def( "time", paste0("days since ", data$Dates$start[1]), times, unlim=FALSE, calendar="gregorian", create_dimvar = TRUE)
-  dimlon  <- ncdim_def( "lon", units="degrees_east", data$xyCoords$x, longname="longitude", create_dimvar = TRUE)
-  dimlat  <- ncdim_def( "lat", units="degrees_north", data$xyCoords$y, longname="latitude", create_dimvar = TRUE)
-  if (length(member.index)>0){
-    dimens  <- ncdim_def( "member", units="member", 0:(dim(data$Data)[member.index]-1), longname="realization", create_dimvar = TRUE)
-    perOrdered <- c(lon.index,lat.index,member.index,time.index)
-    dimOrdered <- list(dimlon,dimlat,dimens,dimtime)
-  }else{
-    perOrdered <- c(lon.index,lat.index,time.index)
-    dimOrdered <- list(dimlon,dimlat,dimtime)
-  }
-  dataOrdered <- aperm(data$Data, perOrdered)
-  var <- ncvar_def(data$Variable$varName, units=tmpUnits, dim=dimOrdered, missval, longname=tmpStdName, compression=compression, shuffle = shuffle)
-  ncnew <- nc_create(NetCDFOutFile, var )
-  ncatt_put(ncnew, "time", "standard_name","time")
-  ncatt_put(ncnew, "time", "axis","T")
-  ncatt_put(ncnew, "time", "_CoordinateAxisType","Time")
-  ncatt_put(ncnew, "time", "_ChunkSize",1)
-  ncatt_put(ncnew, "lon", "standard_name","longitude")
-  ncatt_put(ncnew, "lon", "_CoordinateAxisType","Lon")
-  ncatt_put(ncnew, "lat", "standard_name","latitude")
-  ncatt_put(ncnew, "lat", "_CoordinateAxisType","Lat")
-  if (length(member.index)>0){
-    ncatt_put(ncnew, "member", "standard_name","realization")
-    ncatt_put(ncnew, "member", "_CoordinateAxisType","Ensemble")
-    ncatt_put(ncnew, "member", "ref","http://www.uncertml.org/samples/realisation")
-  }
-  ncatt_put(ncnew, data$Variable$varName, "missing_value",missval)
-  for (v in 1:length(varAttributes)){
-    ncatt_put(ncnew, data$Variable$varName, names(varAttributes)[v],as.character(varAttributes[v]))
-  }
-  for (v in 1:length(globalAttributes)){
-    ncatt_put(ncnew, 0, names(globalAttributes)[v],as.character(globalAttributes[v]))
-  }
-  if (length(attr(data$Data, "correction"))>0){
-    ncatt_put(ncnew, 0, "product","Bias-Correction")
-    ncatt_put(ncnew, 0, "bc_method",attr(data$Data, "correction"))
-  }
-  if (length(attr(data, "dataset"))>0){
-    ncatt_put(ncnew, 0, "dataset",attr(data, "dataset"))
-  }
-  if (length(attr(data, "source"))>0){
-    ncatt_put(ncnew, 0, "source",attr(data, "source"))
-  }
-  ncatt_put(ncnew, 0, "description","NetCDF file created by downscaleR: https://github.com/SantanderMetGroup/downscaleR")
-  ncatt_put(ncnew, 0, "Conventions","CF-1.4")
-  ncvar_put(ncnew, var, dataOrdered )
-  nc_close(ncnew)
-  message(paste0("NetCDF file written: ", NetCDFOutFile))
+grid2NetCDF <- function(data, NetCDFOutFile = "out.nc4", missval = 1e20, globalAttributes = NULL, varAttributes = NULL, prec = "float", compression=4, shuffle = TRUE) {
+      data(vocabulary)
+      ntime<-length(data$Dates$start)
+      tmpStdName<-as.character(vocabulary$standard_name[pmatch(vocabulary$identifier,data$Variable$varName, nomatch=0) > 0])
+      tmpUnits<-as.character(vocabulary$units[pmatch(vocabulary$identifier,data$Variable$varName, nomatch=0) > 0])
+      time.index <- grep("^time$", attr(data$Data, "dimensions"))
+      lon.index <- grep("^lon$", attr(data$Data, "dimensions"))
+      lat.index <- grep("^lat$", attr(data$Data, "dimensions"))
+      member.index <- grep("^member$", attr(data$Data, "dimensions"))
+      datesList <- as.POSIXct(data$Dates$start, tz="GMT", format="%Y-%m-%d %H:%M:%S")
+      times <- (as.double(datesList)-as.double(datesList[1]))/86400
+      dimtime <- ncdim_def( "time", paste0("days since ", data$Dates$start[1]), times, unlim=FALSE, calendar="gregorian", create_dimvar = TRUE)
+      dimlon  <- ncdim_def( "lon", units="degrees_east", data$xyCoords$x, longname="longitude", create_dimvar = TRUE)
+      dimlat  <- ncdim_def( "lat", units="degrees_north", data$xyCoords$y, longname="latitude", create_dimvar = TRUE)
+      if (length(member.index)>0){
+            dimens  <- ncdim_def( "member", units="member", 0:(dim(data$Data)[member.index]-1), longname="realization", create_dimvar = TRUE)
+            perOrdered <- c(lon.index,lat.index,member.index,time.index)
+            dimOrdered <- list(dimlon,dimlat,dimens,dimtime)
+      }else{
+            perOrdered <- c(lon.index,lat.index,time.index)
+            dimOrdered <- list(dimlon,dimlat,dimtime)
+      }
+      dataOrdered <- aperm(data$Data, perOrdered)
+      var <- ncvar_def(data$Variable$varName, units=tmpUnits, dim=dimOrdered, missval, longname=tmpStdName, compression=compression, shuffle = shuffle)
+      ncnew <- nc_create(NetCDFOutFile, var )
+      ncatt_put(ncnew, "time", "standard_name","time")
+      ncatt_put(ncnew, "time", "axis","T")
+      ncatt_put(ncnew, "time", "_CoordinateAxisType","Time")
+      ncatt_put(ncnew, "time", "_ChunkSize",1)
+      ncatt_put(ncnew, "lon", "standard_name","longitude")
+      ncatt_put(ncnew, "lon", "_CoordinateAxisType","Lon")
+      ncatt_put(ncnew, "lat", "standard_name","latitude")
+      ncatt_put(ncnew, "lat", "_CoordinateAxisType","Lat")
+      if (length(member.index)>0){
+            ncatt_put(ncnew, "member", "standard_name","realization")
+            ncatt_put(ncnew, "member", "_CoordinateAxisType","Ensemble")
+            ncatt_put(ncnew, "member", "ref","http://www.uncertml.org/samples/realisation")
+      }
+      ncatt_put(ncnew, data$Variable$varName, "missing_value",missval)
+      for (v in 1:length(varAttributes)){
+            ncatt_put(ncnew, data$Variable$varName, names(varAttributes)[v],as.character(varAttributes[v]))
+      }
+      for (v in 1:length(globalAttributes)){
+            ncatt_put(ncnew, 0, names(globalAttributes)[v],as.character(globalAttributes[v]))
+      }
+      if (length(attr(data$Data, "correction"))>0){
+            ncatt_put(ncnew, 0, "product","Bias-Correction")
+            ncatt_put(ncnew, 0, "bc_method",attr(data$Data, "correction"))
+      }
+      if (length(attr(data, "dataset"))>0){
+            ncatt_put(ncnew, 0, "dataset",attr(data, "dataset"))
+      }
+      if (length(attr(data, "source"))>0){
+            ncatt_put(ncnew, 0, "source",attr(data, "source"))
+      }
+      ncatt_put(ncnew, 0, "description","NetCDF file created by downscaleR: https://github.com/SantanderMetGroup/downscaleR")
+      ncatt_put(ncnew, 0, "Conventions","CF-1.4")
+      ncvar_put(ncnew, var, dataOrdered )
+      nc_close(ncnew)
+      message(paste0("NetCDF file written: ", NetCDFOutFile))
 }
diff --git a/man/aggr6hToDailyMean.Rd b/man/aggr6hToDailyMean.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/aggr6hToDailyMean.R
 \name{aggr6hToDailyMean}
 \alias{aggr6hToDailyMean}
 \title{Performs the aggregation of 6 hourly data to daily mean}

diff --git a/man/analogs.Rd b/man/analogs.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/analogs.R
 \name{analogs}
 \alias{analogs}
 \title{Analog downscaling}

diff --git a/man/array3Dto2Dmat.Rd b/man/array3Dto2Dmat.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/array3Dto2Dmat.R
 \name{array3Dto2Dmat}
 \alias{array3Dto2Dmat}
 \title{Conversion of a 3D array to a 2D matrix}

diff --git a/man/biasCorrection.Rd b/man/biasCorrection.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/biasCorrection.R
 \name{biasCorrection}
 \alias{biasCorrection}
 \title{Bias correction methods}

diff --git a/man/bubbleValidation.Rd b/man/bubbleValidation.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/bubbleValidation.R
 \name{bubbleValidation}
 \alias{bubbleValidation}
 \title{Bubble plot for visualization of the skill of an ensemble forecast prediction}

diff --git a/man/calibrateProj.Rd b/man/calibrateProj.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/biasCorrection.R
 \name{calibrateProj}
 \alias{calibrateProj}
 \title{Bias correction methods}

diff --git a/man/dataInventory.ASCII.Rd b/man/dataInventory.ASCII.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/dataInventory.R
 \name{dataInventory.ASCII}
 \alias{dataInventory.ASCII}
 \title{Data inventory of standard ASCII station datasets}

diff --git a/man/dataInventory.NetCDF.Rd b/man/dataInventory.NetCDF.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/dataInventory.R
 \name{dataInventory.NetCDF}
 \alias{dataInventory.NetCDF}
 \title{Inventory of a gridded dataset}

diff --git a/man/dataInventory.Rd b/man/dataInventory.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/dataInventory.R
 \name{dataInventory}
 \alias{dataInventory}
 \title{Dataset inventory}

diff --git a/man/dateReplacement.Rd b/man/dateReplacement.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/misc.R
 \name{dateReplacement}
 \alias{dateReplacement}
 \title{Compute dates of a downscaled observational dataset}

diff --git a/man/deaccum.Rd b/man/deaccum.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/deaccum.R
 \name{deaccum}
 \alias{deaccum}
 \title{Performs deaccumulation}

diff --git a/man/dictionaryLookup.Rd b/man/dictionaryLookup.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/dictionaryLookup.R
 \name{dictionaryLookup}
 \alias{dictionaryLookup}
 \title{Searches variable string in the dictionary}

diff --git a/man/dictionaryTransform.Rd b/man/dictionaryTransform.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/dictionaryTransform.R
 \name{dictionaryTransform}
 \alias{dictionaryTransform}
 \title{Performs variable transformation}

diff --git a/man/dictionaryTransformGrid.Rd b/man/dictionaryTransformGrid.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/dictionaryTransformGrid.R
 \name{dictionaryTransformGrid}
 \alias{dictionaryTransformGrid}
 \title{Performs variable transformation}

diff --git a/man/fieldFromPCs.Rd b/man/fieldFromPCs.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/fieldFromPCs.R
 \name{fieldFromPCs}
 \alias{fieldFromPCs}
 \title{Reconstruct a Field from EOFs and principal components}

diff --git a/man/findPointXYindex.Rd b/man/findPointXYindex.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/findPointXYindex.R
 \name{findPointXYindex}
 \alias{findPointXYindex}
 \title{Define user-defined geolocation parameters}

diff --git a/man/findVerticalLevel.Rd b/man/findVerticalLevel.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/findVerticalLevel.R
 \name{findVerticalLevel}
 \alias{findVerticalLevel}
 \title{Finds vertical level from variable definition}

diff --git a/man/getCoordinates.Rd b/man/getCoordinates.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/misc.R
 \name{getCoordinates}
 \alias{getCoordinates}
 \title{Get geographical coordinates of a climate data object}

diff --git a/man/getGrid.Rd b/man/getGrid.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/getGrid.R
 \name{getGrid}
 \alias{getGrid}
 \title{Get regular grid definition}

diff --git a/man/getLatLonDomain.Rd b/man/getLatLonDomain.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/getLatLonDomain.R
 \name{getLatLonDomain}
 \alias{getLatLonDomain}
 \title{Determine the geo-location parameters of an arbitrary user selection}

diff --git a/man/getLatLonDomainStations.Rd b/man/getLatLonDomainStations.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/getLatLonDomainStations.R
 \name{getLatLonDomainStations}
 \alias{getLatLonDomainStations}
 \title{Define geolocation of station datasets}

diff --git a/man/getSeason.Rd b/man/getSeason.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/misc.R
 \name{getSeason}
 \alias{getSeason}
 \title{Get season from a station or field object}

diff --git a/man/getTimeDomain.Rd b/man/getTimeDomain.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/getTimeDomain.R
 \name{getTimeDomain}
 \alias{getTimeDomain}
 \title{Selection of time slices of gridded datasets}

diff --git a/man/getTimeDomainStations.Rd b/man/getTimeDomainStations.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/getTimeDomainStations.R
 \name{getTimeDomainStations}
 \alias{getTimeDomainStations}
 \title{Time  index positions for station dataset selections}

diff --git a/man/getVerticalLevelPars.Rd b/man/getVerticalLevelPars.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/getVerticalLevelPars.R
 \name{getVerticalLevelPars}
 \alias{getVerticalLevelPars}
 \title{Definition of vertical dimension slices}

diff --git a/man/getYearsAsINDEX.Rd b/man/getYearsAsINDEX.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.2): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/misc.R
 \name{getYearsAsINDEX}
 \alias{getYearsAsINDEX}
 \title{Get years as a factor}