Prepared for release of v0.0.0

.Rbuildignore

+.git
+.gitignore
+.tar.gz
+.pdf
+./.nc

DESCRIPTION

@@ -10,8 +10,6 @@ Depends:
 Imports:
     ncdf4,
     abind
-Suggests:
-    startR
 License: LGPL-3
 URL: https://earth.bsc.es/gitlab/es/easyNCDF/wikis/home
 BugReports: https://earth.bsc.es/gitlab/es/easyNCDF/issues

R/ArrayToNc.R

@@ -318,3 +318,5 @@ ArrayToNc <- function(arrays, file_path) {
   nc_close(ncdf_object)
   invisible(NULL)
 }
+
+a2nc <- ArrayToNc

R/NcReadDims.R

@@ -49,6 +49,7 @@ NcReadDims <- function(file_to_read, var_names = NULL) {
       if (!is.null(dims)) {
         dims <- .MergeArrayDims(dims, found_dims)
         dims <- pmax(dims[[1]], dims[[2]])
+        dims['var'] <- dims['var'] + 1
       } else {
         dims <- found_dims
       }

R/NcToArray.R

@@ -203,12 +203,14 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
             #  }
             #  missing_dims <- missing_dim_names
             #}
-            indices_dims <- names(dim_indices)[which(names(dim_indices) %in% names(found_dims))]
             reorder_back <- NULL
-            if (any(names(found_dims) != indices_dims)) {
-              #reorder <- sapply(names(found_dims), function(x) which(indices_dims == x))
-              reorder_back <- sapply(indices_dims, function(x) which(names(found_dims) == x))
-              #indices_to_take <- indices_to_take[reorder]
+            indices_dims <- names(dim_indices)[which(names(dim_indices) %in% names(found_dims))]
+            if (length(indices_dims) > 0) {
+              if (any(names(found_dims) != indices_dims)) {
+                #reorder <- sapply(names(found_dims), function(x) which(indices_dims == x))
+                reorder_back <- sapply(indices_dims, function(x) which(names(found_dims) == x))
+                #indices_to_take <- indices_to_take[reorder]
+              }
             }
             start <- sapply(indices_to_take, function(x) if (is_single_na(x)) 1 else min(x))
             count <- sapply(indices_to_take, function(x) if (is_single_na(x)) -1 else max(x) - min(x) + 1)
@@ -219,14 +221,14 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
             if (!is.null(reorder_back)) {
               var_result <- aperm(var_result, reorder_back)
             }
+            names(dim(var_result)) <- names(indices_to_take)[reorder_back]
             #if (!is.null(missing_dims)) {
             #  dim(var_result) <- original_dims
             #}
             if (!is.null(extra_dims)) {
-              dim(var_result) <- dim(var_result)[-which(indices_dims %in% extra_dims)]
+              dim(var_result) <- dim(var_result)[-which(names(indices_to_take) %in% extra_dims)]
             }
             #attr(var_result, 'variables') <- metadata
-            names(dim(var_result)) <- indices_dims
           }
           atts <- file_object$var[[var_name]]
           atts_to_remove <- c('id', 'name', 'ndims', 'natts', 'size', 
@@ -242,7 +244,7 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
           #names(dim(var_result)) <- sapply(file_object$var[[var_name]]$dim, '[[', 'name')
         }
         if (!is.null(var_result)) {
-          if (!drop_var_dim && (length(vars_to_read_vector) == 1)) {
+          if (!drop_var_dim || (length(vars_to_read_vector) == 1)) {
             dim(var_result) <- c(setNames(1, var_tag), dim(var_result))
           }
           attr(var_result, 'variables') <- structure(list(atts), .Names = var_name)

man/NcClose.Rd

@@ -18,6 +18,21 @@ NetCDF object as returned by \code{ncdf4::nc_open}.
 The result of \code{ncdf4::nc_close}.
 }
 \examples{
+# Create an array from R
+file_path <- tempfile(fileext = '.nc')
+a <- array(1:9, dim = c(member = 3, time = 3))
+# Store into a NetCDF twice, as two different variables
+ArrayToNc(list(var_1 = a, var_2 = a + 1), file_path)
+# Read the dimensions and variables in the created file
+fnc <- NcOpen(file_path)
+fnc_dims <- NcReadDims(fnc)
+var_names <- NcReadVarNames(fnc)
+# Read the two variables from the file into an R array
+a_from_file <- NcToArray(fnc, vars_to_read = var_names)
+NcClose(fnc)
+# Check the obtained array matches the original array
+print(a)
+print(a_from_file[1, , ])
 }
 \author{
 History:\cr

man/NcOpen.Rd

@@ -18,6 +18,21 @@ Character string with the path to the file to be opened.
 A NetCDF object as returned by \code{ncdf4::nc_open} or NULL on failure.
 }
 \examples{
+# Create an array from R
+file_path <- tempfile(fileext = '.nc')
+a <- array(1:9, dim = c(member = 3, time = 3))
+# Store into a NetCDF twice, as two different variables
+ArrayToNc(list(var_1 = a, var_2 = a + 1), file_path)
+# Read the dimensions and variables in the created file
+fnc <- NcOpen(file_path)
+fnc_dims <- NcReadDims(fnc)
+var_names <- NcReadVarNames(fnc)
+# Read the two variables from the file into an R array
+a_from_file <- NcToArray(fnc, vars_to_read = var_names)
+NcClose(fnc)
+# Check the obtained array matches the original array
+print(a)
+print(a_from_file[1, , ])
 }
 \author{
 History:\cr

man/NcReadDims.Rd

@@ -21,6 +21,21 @@ Vector of character strings with the names of the variables which to read the di
 Named numeric vector with the names and sizes of the dimensions for the requested variables.
 }
 \examples{
+# Create an array from R
+file_path <- tempfile(fileext = '.nc')
+a <- array(1:9, dim = c(member = 3, time = 3))
+# Store into a NetCDF twice, as two different variables
+ArrayToNc(list(var_1 = a, var_2 = a + 1), file_path)
+# Read the dimensions and variables in the created file
+fnc <- NcOpen(file_path)
+fnc_dims <- NcReadDims(fnc)
+var_names <- NcReadVarNames(fnc)
+# Read the two variables from the file into an R array
+a_from_file <- NcToArray(fnc, vars_to_read = var_names)
+NcClose(fnc)
+# Check the obtained array matches the original array
+print(a)
+print(a_from_file[1, , ])
 }
 \author{
 History:\cr

man/NcReadVarNames.Rd

@@ -18,6 +18,21 @@ Path to the file to be read or a NetCDF object as returned by \code{easyNCDF::Nc
 Vector of character strings with the names of the variables in the NetCDF file.
 }
 \examples{
+# Create an array from R
+file_path <- tempfile(fileext = '.nc')
+a <- array(1:9, dim = c(member = 3, time = 3))
+# Store into a NetCDF twice, as two different variables
+ArrayToNc(list(var_1 = a, var_2 = a + 1), file_path)
+# Read the dimensions and variables in the created file
+fnc <- NcOpen(file_path)
+fnc_dims <- NcReadDims(fnc)
+var_names <- NcReadVarNames(fnc)
+# Read the two variables from the file into an R array
+a_from_file <- NcToArray(fnc, vars_to_read = var_names)
+NcClose(fnc)
+# Check the obtained array matches the original array
+print(a)
+print(a_from_file[1, , ])
 }
 \author{
 History:\cr

man/NcToArray.Rd

@@ -49,6 +49,21 @@ Whether to allow indices out of range (simply disregard them) or to stop if indi
 Array or list of arrays with the data for one or more than one of the requested variables (depending on the parameters). The dimensions are named. The arrays contain the attribute 'variables' with the metadata items found in the NetCDF file.
 }
 \examples{
+# Create an array from R
+file_path <- tempfile(fileext = '.nc')
+a <- array(1:9, dim = c(member = 3, time = 3))
+# Store into a NetCDF twice, as two different variables
+ArrayToNc(list(var_1 = a, var_2 = a + 1), file_path)
+# Read the dimensions and variables in the created file
+fnc <- NcOpen(file_path)
+fnc_dims <- NcReadDims(fnc)
+var_names <- NcReadVarNames(fnc)
+# Read the two variables from the file into an R array
+a_from_file <- NcToArray(fnc, vars_to_read = var_names)
+NcClose(fnc)
+# Check the obtained array matches the original array
+print(a)
+print(a_from_file[1, , ])
 }
 \author{
 History:\cr

man/Subset.Rd

@@ -40,5 +40,9 @@ FALSE, 'selected', and 'non-selected'.
   }
 }
 \examples{
+# Create an array from R with data for 3 'var', 3 'member' and 3 'time'
+a <- array(1:27, dim = c(var = 3, member = 3, time = 3))
+# Take a subset with all 'member' and 'time' for the 1st 'var'
+b <- Subset(a, 'var', 1)
 }
 \keyword{dplot}