Switched from [ to [[

NAMESPACE

@@ -35,6 +35,8 @@ exportClasses(H5Group)
 exportClasses(H5Location)
 exportMethods("[")
 exportMethods("[<-")
+exportMethods("[[")
+exportMethods("[[<-")
 exportMethods("h5attr<-")
 exportMethods(c)
 exportMethods(createAttribute)

R/CommonFG.R

@@ -12,11 +12,11 @@
 #' specifies the group to be created/accesses and the second the dataset name.
 #' 
 #' Groups can be created/accessed by simply using one character parameter, e.g.
-#' \code{group <- obj["groupname"]}.
+#' \code{group <- obj[["groupname"]]}.
 #' 
 #' DataSets can be either accessed by using  
-#' \code{dset <- obj["groupname", "datasetname"]} if existing or initialized by
-#' using \code{obj["groupname", "datasetname"] <- value}.
+#' \code{dset <- obj[["groupname", "datasetname"]]} if existing or initialized by
+#' using \code{obj[["groupname", "datasetname"]] <- value}.
 #' 
 #' All created objects e.g. \code{group} or \code{dset} should be closed in the
 #' end using \code{h5close}.
@@ -36,13 +36,13 @@
 #' @examples
 #' file <- h5file("test.h5")
 #' # Create new DataSet 'testset' in H5Group 'testgroup'
-#' file["testgroup/testset"] <- matrix(1:9, nrow = 3)
+#' file[["testgroup/testset"]] <- matrix(1:9, nrow = 3)
 #' # Create new DataSet 'testset2' in file root
-#' file["testset2"] <- 1:10
+#' file[["testset2"]] <- 1:10
 #' # Retrieve H5Group 'testgroup'
-#' group <- file["testgroup"]
+#' group <- file[["testgroup"]]
 #' # Retrieve DataSet 'testset'
-#' dset <- group["testset"]
+#' dset <- group[["testset"]]
 #' h5close(dset)
 #' h5close(group)
 #' h5close(file)
@@ -59,7 +59,7 @@ setGeneric("h5close", function(.Object)
 
 #' @rdname CommonFG
 #' @export
-setMethod("[", c("CommonFG", "character", "ANY"),
+setMethod("[[", c("CommonFG", "character", "ANY"),
   function(x, i, ..., drop=TRUE) { 
     if(length(i) > 1) {
       stop("Only one path can be specified.")
@@ -84,7 +84,7 @@ setMethod("[", c("CommonFG", "character", "ANY"),
 #' @param value vector/matrix/array; Value to be assigend to dataset
 #' @rdname CommonFG
 #' @export
-setMethod("[<-", c("CommonFG", "character", "ANY"),
+setMethod("[[<-", c("CommonFG", "character", "ANY"),
   function(x, i, ..., value) {
     if(length(i) > 1) {
       stop("Only one path can be specified.")
@@ -129,3 +129,32 @@ setMethod( "h5unlink", signature(.Object="CommonFG", path="character"),
     }, USE.NAMES = FALSE)
 })
 
+#' Deprecated CommonFG methods
+#' 
+#' Since \code{obj[name]} is commonly used to get and set multiple elements,
+#' \code{obj[[name]]} is the better fit for setting or retrieving a single dataset or groups.
+#' 
+#' @param x,i,j,drop,value,...  See \code{\link{CommonFG}}
+#' 
+#' @name h5-deprecated
+#' @rdname h5-deprecated
+#' @export
+setMethod("[", c("CommonFG", "character", "ANY"),
+  function(x, i, ..., drop=TRUE) {
+    var <- deparse(substitute(x))
+    key <- deparse(substitute(i))
+    .Deprecated("[[", msg = sprintf("Use %s[[%s]] instead of %s[%s]", var, key, var, key))
+    x[[i, ..., drop = drop]]
+  })
+
+#' @rdname h5-deprecated
+#' @export
+setMethod("[<-", c("CommonFG", "character", "ANY"),
+  function(x, i, ..., value) {
+    # deparse(substitute(x)) sadly returns '*tmp*'
+    key <- deparse(substitute(i))
+    val <- deparse(substitute(value))
+    .Deprecated("[[<-", msg = sprintf("Use x[[%s]] <- %s instead of x[%s] <- %s", key, val, key, val))
+    x[[i, ...]] <- value
+    x
+  })

R/Dataset-Subset.R

@@ -22,9 +22,9 @@
 #' # Write submatrix to sub-region of DataSet
 #' testmat_n <- matrix(as.integer(1:90), ncol = 9)
 #' file <- h5file("test.h5", "a")
-#' file["testgroup/testmat_n2"] <- testmat_n
+#' file[["testgroup/testmat_n2"]] <- testmat_n
 #' submat <- matrix(-1L:-9L, nrow = 3)
-#' dset2 <- file["testgroup/testmat_n2"]
+#' dset2 <- file[["testgroup/testmat_n2"]]
 #' dset2[c(1, 3, 5), c(1, 3, 5)] <- submat
 #' h5close(dset2)
 #' h5close(file)

R/H5File.R

@@ -73,25 +73,25 @@
 #' # The following examples generates a HDF5 file with the different HDF5 
 #' # Objects and shows its contents:
 #' file <- h5file(name = "test1.h5", mode = "a")
-#' file["testdataset"] <- 1:10
+#' file[["testdataset"]] <- 1:10
 #' h5attr(file, "testattrib") <- LETTERS[1:10]
-#' file["testgroup/testdataset2"] <- 1:10
+#' file[["testgroup/testdataset2"]] <- 1:10
 #' file
 #' # Close file and delete
 #' h5close(file)
 #' if(file.exists("test.h5")) file.remove("test.h5")
 #' 
 #' # The following example shows hdf5 file contents and how to use them to iterate over HDF5 elements:
 #' file <- h5file(name = "test2.h5", mode = "a")
-#' file["testgroup1/testset1"] <- 1:10
-#' file["testgroup2/testset2"] <- 11:20
-#' file["testgroup3/testset3"] <- 21:30
+#' file[["testgroup1/testset1"]] <- 1:10
+#' file[["testgroup2/testset2"]] <- 11:20
+#' file[["testgroup3/testset3"]] <- 21:30
 #' 
 #' # Extract first 3 elements from each dataset and combine result to matrix
 #' sapply(list.datasets(file, recursive = TRUE), function(x) file[x][1:3])
 #' # Add new dataset to each group in HDF5 file
 #' for(g in list.groups(file)) {
-#'   file[paste(g, "testsetx", collapse = "/")] <- 1:10
+#'   file[[paste(g, "testsetx", collapse = "/")]] <- 1:10
 #' }
 #' list.datasets(file, recursive = TRUE)
 #' # Close file

R/H5Location-Attribute.R

@@ -16,11 +16,11 @@
 #' # Write Attributes for H5File, H5Group and DataSet
 #' file <- h5file("test.h5")
 #' h5attr(file, "fileattrib") <- 1:10
-#' group <- file["testgroup"]
+#' group <- file[["testgroup"]]
 #' h5attr(group, "groupattrib") <- matrix(1:9, nrow = 3)
 #' h5attr(group, "groupattrib")
 #' group["testdataset"] <- 1:10
-#' dset <- group["testdataset"]
+#' dset <- group[["testdataset"]]
 #' h5attr(dset, "dsetattrib") <- LETTERS[1:10]
 #' h5close(dset)
 #' h5close(group)

R/h5-package.R

@@ -75,13 +75,13 @@
 #' mat <- matrix(1:9, nrow = 3)
 #' rownames(mat) <- LETTERS[1:3]
 #' colnames(mat) <- c("A", "BE", "BUU")
-#' file["test/testmat/testmat"] <- mat
+#' file[["test/testmat/testmat"]] <- mat
 #' # Store numeric array in group '/test' and dataset 'testarray'
-#' file["test/testarray"] <- array(as.numeric(1:45), dim = c(3, 3, 5))
+#' file[["test/testarray"]] <- array(as.numeric(1:45), dim = c(3, 3, 5))
 #' 
 #' # 3. Store rownames and column names of matrix as attributes
 #' # Get created data set as object
-#' dset <- file["test/testmat/testmat"]
+#' dset <- file[["test/testmat/testmat"]]
 #' # Store rownames in attribute 'dimnames_1'
 #' h5attr(dset, "dimnames_1") <- rownames(mat)
 #' # Store columnnames in attribute 'dimnames_2'