.gitignore

@@ -16,4 +16,4 @@ ignore
 .Rbuildignore
 .Rprofile
 .directory
-
+.DS_Store

DESCRIPTION

@@ -1,36 +1,35 @@
 Package: loadeR
 Depends:
-    R(>= 3.1.0),
+    R(>= 3.5.0),
     rJava,
-    loadeR.java
+    loadeR.java,
+    climate4R.UDG(>= 0.2.0)
 Imports:
     utils,
     abind,
     RCurl
 Suggests:
-    loadeR.ECOMS,
     transformeR,
     visualizeR,
     downscaleR
 Type: Package
 Title: A climate4R package for data access <http://meteo.unican.es/climate4r>
-Version: 1.4.15
-Date: 2019-07-30
-Authors@R: as.person(c(
-    "Santander Meteorology Group <http://meteo.unican.es> [cph]",
-    "Joaquín Bedia <bediaj@unican.es> [aut,cre]",
-    "Antonio Cofiño <antonio.cofino@unican.es> [ctb]",
-    "Matteo de Felice <matteo.defelice@enea.it> [ctb]",
-    "Jesus Fernández <fernandej@unican.es> [ctb]",
-    "José Manuel Gutiérrez <gutierjm@unican.es> [ctb]",
-    "Sixto Herrera <herreras@unican.es> [ctb]",
-    "Maialen Iturbide <miturbide@ifca.unican.es> [aut]",
-    "Etienne Tourigny <etienne.tourigny@bsc.es> [ctb]",
-    "Max Tuni <max@predictia.es> [ctb]",
-    "Manuel Vega <manuel.vega@unican.es> [ctb]"))
+Version: 1.8.2
+Date: 2024-06-04
+Authors@R: c(person("Bedia", "Joaquín", email = "bediaj@unican.es", role = c("aut","cre"), comment = c(ORCID = "0000-0001-6219-4312")),
+             person("Antonio", "Cofiño", email = "antonio.cofino@unican.es", role = "ctb"),
+             person("Matteo", "de Felice", email = "matteo.defelice@enea.it", role = "ctb"),
+             person("Jesús", "Fernández", email = "fernandej@unican.es", role = "ctb"),
+             person("José Manuel", "Gutiérrez", email = "gutierjm@unican.es", role = "ctb"),
+             person("Sixto", "Herrera", email = "herreras@unican.es", role = "aut"),
+             person("Maialen", "Iturbide", email = "miturbide@ifca.unican.es", role = "aut", comment = c(ORCID = "0000-0002-5048-0941")),
+             person("Etienne", "Tourigny", email = "etienne.tourigny@bsc.es", role = "ctb"),
+             person("Max", "Tuni", email = "max@predictia.es", role = "ctb"),
+             person("Manuel", "Vega", email = "manuel.vega@unican.es", role = "ctb"),
+             person("Santander Meteorology Group", comment = "<http://www.meteo.unican.es/en>", role = "cph"))
 BugReports: https://github.com/SantanderMetGroup/loadeR/issues
 URL: https://github.com/SantanderMetGroup/loadeR/wiki
 Encoding: UTF-8
 Description: Enables harmonized access to either remote climate databases via OPeNDAP or to locally stored data, allowing the retrieval of user-defined dimensional slices from large climate datasets. For more details see Iturbide et al 2019 <http://dx.doi.org/10.1016/j.envsoft.2018.09.009>.
 License: file LICENSE
-RoxygenNote: 6.1.1
+RoxygenNote: 7.3.1

NAMESPACE

@@ -1,8 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(C4R.vocabulary)
-export(C4R.vocabulary.update)
-export(UDG.datasets)
+export(C4R.datasets)
 export(adjustDates)
 export(adjustDates.forecast)
 export(adjustRCMgrid)
@@ -24,7 +22,6 @@ export(loadGridData)
 export(loadGridDataset)
 export(loadSeasonalForecast)
 export(loadStationData)
-export(loginUDG)
 export(makeAggregatedDataset)
 export(makeSubset)
 export(mslp2ps)
@@ -40,17 +37,19 @@ export(writeStationData)
 importFrom(RCurl,getURL)
 importFrom(RCurl,url.exists)
 importFrom(abind,abind)
+importFrom(climate4R.UDG,C4R.vocabulary)
+importFrom(climate4R.UDG,UDG.datasets)
 importFrom(graphics,lines)
 importFrom(graphics,text)
 importFrom(loadeR.java,javaCalendarDate2rPOSIXlt)
 importFrom(loadeR.java,javaString2rChar)
 importFrom(rJava,.jnew)
 importFrom(rJava,.jnull)
 importFrom(rJava,J)
+importFrom(stats,median)
 importFrom(stats,na.exclude)
 importFrom(stats,na.omit)
 importFrom(stats,setNames)
-importFrom(utils,URLencode)
 importFrom(utils,globalVariables)
 importFrom(utils,head)
 importFrom(utils,packageDescription)
@@ -59,4 +58,3 @@ importFrom(utils,read.csv)
 importFrom(utils,tail)
 importFrom(utils,unzip)
 importFrom(utils,write.csv)
-importFrom(utils,write.table)

NEWS

@@ -67,5 +67,36 @@ For earlier version changes, see the GitHub Releases [Tab](https://github.com/Sa
 ## v1.4.15 (30 Jul 2019)
  * Bug fix related to loading datasets that contain the level dimension
 
-
-
+## v1.5.0 (13 Aug 2019)
+ * Functions loginUDG, UDG.datasets and C4R.vocabulary deprecated and now available in package climate4R.UDG
+
+## v1.6.0 (5 Jan 2020)
+ * Add climate4R.UDG dependency (for accessing UDG datasets)
+ * Do not allow requests of years out of boundaries in loadGridData
+
+## v1.6.1 (23 Mar 2020) 
+ * Minor bug fixes and and enhancements
+
+## v1.7.0 (18 Sep 2020)
+ * Enhancements in NetCDF support for loading station datasets via loadStationData
+ * Several improvements and bug fixes in loadGridData for rotated grids
+ * Include 'Shape' and 'MemorySizeMb' attributes in dataInventory for NetCDF datasets
+ * Include 2D coordinates of irregular grids in dataInventories
+ * Minor bug fixes and enhancements for dealing with ensemble axes
+ * loginUDG, C4R.vocabulary and C4R.vocabulary.update utilities moved to climate4R.UDG dependency
+ * Other minor bug fixes and documentation updates
+
+## v1.7.1 (05 Jul 2021) 
+ * Minor bug fixes and and enhancements
+
+## v1.8.0 (21 Jun 2023) 
+ * Minor fix in loadSeasonalForecast output attributes (resX and resY)
+ * Bug fix in dataInventory: exact variable name retrieval by grep
+ * Adapt to new class denomination for matrix objects in R version 4.X
+
+## v1.8.1 (22 Jun 2023) 
+ * Update of the DESCRIPTION file 
+
+## v1.8.2 (04 Jun 2024) 
+ * Minor changes in loadSeasonalForecast to handle non-standard dimension names
+

R/dataInventory.NetCDF.R

@@ -0,0 +1,103 @@
+#' @title Inventory of a gridded dataset
+#' @description Returns a list with summary information about the variables stored in a gridded dataset.
+#' Sub-routine of \code{dataInventory}
+#' @param dataset A full path to the file describing the dataset (NcML)
+#' @return A (named) list whose length is determined by the number of variables stored in the dataset,
+#' its names corresponding to the short names of the variables.
+#' For each variable, information on the variable long name, data type, units, data size (in Mb) and
+#' characteristics of its dimensions is provided.
+#' @author J. Bedia, S. Herrera
+#' @keywords internal
+#' @importFrom rJava J
+
+
+dataInventory.NetCDF <- function(dataset) {
+   gds <- J("ucar.nc2.dt.grid.GridDataset")$open(dataset)
+   nc.dataset <- gds$getNetcdfDataset()
+   varNames <- unlist(strsplit(gsub("\\[|]|\\s", "", gds$getGrids()$toString()), ","))
+   rm.ind <- grep("^lon|^lat", varNames)  
+   if (length(rm.ind) > 0) {
+      varNames <- varNames[-rm.ind]
+   }
+   if (length(varNames) == 0) {
+      stop("No variables found", call. = FALSE)
+   } else {
+      var.list <- vector(mode = "list", length = length(varNames))   
+      for (i in 1:length(varNames)) {
+         message("[", Sys.time(), "] Retrieving info for \'", varNames[i], "\' (", length(varNames) - i, " vars remaining)")
+         datavar <- gds$getDataVariable(varNames[i])
+         description <- datavar$getDescription()
+         varName <- datavar$getShortName()
+         version <- tryCatch({trimws(datavar$findAttribute("version")$getValues()$toString())}, error = function(e){NA})
+         dataType <- datavar$getDataType()$toString()
+         element.size <- datavar$getDataType()$getSize()
+         data.number <- datavar$getSize()
+         dataSize <- element.size * data.number * 1e-06
+         units <- datavar$getUnitsString()
+         shape <- datavar$getShape()
+         grid <- gds$findGridByShortName(varName)
+         dim.list <- scanVarDimensions(grid)
+         if (grid$getXDimensionIndex() >= 0) {
+           xDimIndex <- grid$getXDimensionIndex() + 1
+           if (length(dim.list[[xDimIndex]]$Shape) > 1) {
+             dimX.list <- list()
+             length(dimX.list) <- length(dim.list[[xDimIndex]]$Shape)
+             for (v in c(1:length(dimX.list))) {
+                dimX.list[[v]] <- tryCatch({
+                   Xcoord <- nc.dataset$findVariable(dim.list[[xDimIndex]]$Coordinates[v])
+                   Xunits <- Xcoord$getUnitsString()
+                   XType <- Xcoord$getAxisType()$toString()
+                   XAxisShape <- Xcoord$getShape()
+                   values <- Xcoord$getCoordValues()
+                   aux.XAxis <- Xcoord$getDimensionsString()
+                   list("Type" = XType, "Units" = Xunits,
+                        "Values" = values, "Shape" =  XAxisShape,"Coordinates" = aux.XAxis)
+                }, error = function(e) {
+                   list("Type" = NULL, "Units" = NULL,
+                        "Values" = NULL, "Shape" =  NULL,
+                        "Coordinates" = NULL)
+                   })
+                names(dimX.list)[v] <- dim.list[[xDimIndex]]$Coordinates[v] # "lon"
+             }
+             dim.list[[xDimIndex]]$Dimensions <- dimX.list
+           }
+         }
+         if (grid$getYDimensionIndex() >= 0) {
+           yDimIndex <- grid$getYDimensionIndex() + 1
+           if (length(dim.list[[yDimIndex]]$Shape) > 1) {
+             dimX.list <- list()
+             length(dimX.list) <- length(dim.list[[yDimIndex]]$Shape)
+             for (v in c(1:length(dimX.list))) {
+                dimX.list[[v]] <- tryCatch({
+                   Xcoord <- nc.dataset$findVariable(dim.list[[yDimIndex]]$Coordinates[v])
+                   Xunits <- Xcoord$getUnitsString()
+                   XType <- Xcoord$getAxisType()$toString()
+                   XAxisShape <- Xcoord$getShape()
+                   values <- Xcoord$getCoordValues()
+                   aux.XAxis <- Xcoord$getDimensionsString()
+                   list("Type" = XType, "Units" = Xunits,
+                        "Values" = values, "Shape" =  XAxisShape,"Coordinates" = aux.XAxis)
+                }, error = function(e) {
+                   list("Type" = NULL, "Units" = NULL,
+                        "Values" = NULL, "Shape" =  NULL,
+                        "Coordinates" = NULL)
+                   })
+                names(dimX.list)[v] <- dim.list[[yDimIndex]]$Coordinates[v] # "lon"
+             }
+             dim.list[[yDimIndex]]$Dimensions <- dimX.list
+           }
+         }
+         var.list[[i]] <- list("Description" = description,
+                               "DataType" = dataType,
+                               "Shape" = shape,
+                               "Units" = units,
+                               "DataSizeMb" = dataSize,
+                               "Version" = version,
+                               "Dimensions" = dim.list)
+      }
+      names(var.list) <- varNames
+   }
+   gds$close()
+   return(var.list)
+}
+# End