Add examples

R/R6Classes_H5A.R

@@ -31,8 +31,23 @@
 ##' @docType class
 ##' @importFrom R6 R6Class
 ##' @return Object of class \code{\link{H5A}}. 
-##' @export
 ##' @author Holger Hoefling
+##' @examples 
+##' fname <- tempfile(fileext = ".h5")
+##' file <- H5File$new(fname, mode = "a")
+##' h5attr(file, "attr_numeric") <- rnorm(10)
+##' a <- file$attr_open("attr_numeric")
+##' a$get_info()
+##' a$attr_name()
+##' a$get_space()
+##' a$get_type()
+##' a$get_storage_size()
+##' a$read()
+##' a$write(10:1)
+##' a$print()
+##' a$close()
+##' file$close_all()
+##' @export
 H5A <- R6Class("H5A",
                inherit=H5RefClass,
                public=list(

R/R6Classes_H5D.R

@@ -61,7 +61,6 @@ setOldClass("H5D")
 ##' @docType class
 ##' @importFrom R6 R6Class
 ##' @return Object of class \code{\link{H5D}}.
-##' @export
 ##' @author Holger Hoefling
 ##' @examples
 ##' # First create a file to create datasets in it
@@ -96,6 +95,7 @@ setOldClass("H5D")
 ##'
 ##' file$close_all()
 ##' file.remove(fname)
+##' @export
 H5D <- R6Class("H5D",
                inherit=H5RefClass,
                public=list(

R/R6Classes_H5Group.R

@@ -33,6 +33,13 @@
 ##' @return Object of class \code{\link{H5Group}}. 
 ##' @export
 ##' @author Holger Hoefling
+##' @examples
+##' fname <- tempfile(fileext = ".h5")
+##' file <- H5File$new(fname, mode = "a")
+##' group <- file$create_group("testgroup")
+##' group$print()
+##' group$close()
+##' file$close_all()
 H5Group <- R6Class("H5Group",
                    inherit=H5RefClass,
                    public=list(

R/R6Classes_H5P.R

@@ -106,8 +106,18 @@ H5P_factory <- function(id) {
 #' @docType class
 #' @importFrom R6 R6Class
 #' @return Object of class \code{\link{H5P}}.
-#' @export
 #' @author Holger Hoefling
+#' @examples 
+#' fname <- tempfile(fileext = ".h5")
+#' file <- H5File$new(fname, mode = "a")
+#' file[["testdataset"]] <- 1:10
+#' p <- file[["testdataset"]]$get_create_plist()
+#' p$get_class()
+#' p$get_class_name()
+#' p$copy()
+#' p$equal(p)
+#' file$close_all()
+#' @export
 H5P <- R6Class("H5P",
                inherit=H5RefClass,
                public=list(

R/R6Classes_H5R.R

@@ -37,8 +37,15 @@ ref_obj_size <- new.env()
 #' @docType class
 #' @importFrom R6 R6Class
 #' @return Object of class \code{\link[=H5R]{H5R}}.
-#' @export
 #' @author Holger Hoefling
+#' @examples
+#' fname <- tempfile(fileext = ".h5")
+#' file <- H5File$new(fname, mode = "a")
+#' file[["testset"]] <- matrix(rnorm(9), nrow = 3)
+#' dset <- file[["testset"]]
+#' r <- file$create_reference("testset")
+#' file$close_all()
+#' @export
 H5R <- R6Class("H5R",
                inherit=H5RefClass,
                public=list(

R/R6Classes_H5S.R

@@ -36,7 +36,6 @@
 ##' @docType class
 ##' @importFrom R6 R6Class
 ##' @return Object of class \code{\link{H5S}}. 
-##' @export
 ##' @author Holger Hoefling
 ##'
 ##' @examples
@@ -58,7 +57,7 @@
 ##' h5s_variable[2:7, 1:2]
 ##' h5s_variable$get_select_type()
 ##' h5s_variable$get_select_hyper_blocklist()
-##' 
+##' @export
 H5S <- R6Class("H5S",
                inherit=H5RefClass,
                public=list(

R/R6Classes_H5T.R

@@ -163,7 +163,6 @@ text_to_dtype <- function(text, lang_type=h5const$H5LT_DDL) {
 #' @docType class
 #' @importFrom R6 R6Class
 #' @return Object of class \code{\link{H5T}}.
-#' @export
 #' @author Holger Hoefling
 #'
 #' @examples
@@ -184,6 +183,7 @@ text_to_dtype <- function(text, lang_type=h5const$H5LT_DDL) {
 #' 
 #' file$close_all()
 #' file.remove(fname)
+#' @export
 H5T <- R6Class("H5T",
                inherit=H5RefClass,
                public=list(

R/hdf5r.R

@@ -36,7 +36,33 @@ NULL
 ##' 
 ##' @name hdf5r-package
 ##' @docType package
-##'
+##' @examples 
+##' test_file <- tempfile(fileext=".h5")
+##' file.h5 <- H5File$new(test_file, mode="w")
+##' 
+##' data(cars)
+##' file.h5$create_group("test")
+##' file.h5[["test/cars"]] <- cars
+##' cars_ds <- file.h5[["test/cars"]]
+##' h5attr(cars_ds, "rownames") <- rownames(cars)
+##' 
+##' # Close the file at the end
+##' # the 'close' method closes only the file-id, but leaves object inside the file open
+##' # This may prevent re-opening of the file. 'close_all' closes the file and all objects in it
+##' file.h5$close_all()
+##' # now re-open it 
+##' file.h5 <- H5File$new(test_file, mode="r+")
+##' 
+##' # lets look at the content
+##' file.h5$ls(recursive=TRUE)
+##' 
+##' cars_ds <- file.h5[["test/cars"]]
+##' # note that for now tables in HDF5 are 1-dimensional, not 2-dimensional
+##' mycars <- cars_ds[]
+##' h5attr_names(cars_ds)
+##' h5attr(cars_ds, "rownames")
+##' 
+##' file.h5$close_all()
 NULL