Remove out-of-date external compatibility section from hdf_store docs (pandas-dev#49088)

* Remove out-of-date external compatibility section from hdf_store docs

* Remove references

Author: ivirshup

doc/source/getting_started/comparison/comparison_with_r.rst

@@ -21,10 +21,6 @@ libraries, we care about the following things:
 This page is also here to offer a bit of a translation guide for users of these
 R packages.
 
-For transfer of ``DataFrame`` objects from pandas to R, one option is to
-use HDF5 files, see :ref:`io.external_compatibility` for an
-example.
-
 
 Quick reference
 ---------------

doc/source/user_guide/io.rst

@@ -5264,99 +5264,6 @@ You could inadvertently turn an actual ``nan`` value into a missing value.
    store.append("dfss2", dfss, nan_rep="_nan_")
    store.select("dfss2")
 
-.. _io.external_compatibility:
-
-External compatibility
-''''''''''''''''''''''
-
-``HDFStore`` writes ``table`` format objects in specific formats suitable for
-producing loss-less round trips to pandas objects. For external
-compatibility, ``HDFStore`` can read native ``PyTables`` format
-tables.
-
-It is possible to write an ``HDFStore`` object that can easily be imported into ``R`` using the
-``rhdf5`` library (`Package website`_). Create a table format store like this:
-
-.. _package website: https://www.bioconductor.org/packages/release/bioc/html/rhdf5.html
-
-.. ipython:: python
-
-   df_for_r = pd.DataFrame(
-       {
-           "first": np.random.rand(100),
-           "second": np.random.rand(100),
-           "class": np.random.randint(0, 2, (100,)),
-       },
-       index=range(100),
-   )
-   df_for_r.head()
-
-   store_export = pd.HDFStore("export.h5")
-   store_export.append("df_for_r", df_for_r, data_columns=df_dc.columns)
-   store_export
-
-.. ipython:: python
-   :suppress:
-
-   store_export.close()
-   os.remove("export.h5")
-
-In R this file can be read into a ``data.frame`` object using the ``rhdf5``
-library. The following example function reads the corresponding column names
-and data values from the values and assembles them into a ``data.frame``:
-
-.. code-block:: R
-
-   # Load values and column names for all datasets from corresponding nodes and
-   # insert them into one data.frame object.
-
-   library(rhdf5)
-
-   loadhdf5data <- function(h5File) {
-
-   listing <- h5ls(h5File)
-   # Find all data nodes, values are stored in *_values and corresponding column
-   # titles in *_items
-   data_nodes <- grep("_values", listing$name)
-   name_nodes <- grep("_items", listing$name)
-   data_paths = paste(listing$group[data_nodes], listing$name[data_nodes], sep = "/")
-   name_paths = paste(listing$group[name_nodes], listing$name[name_nodes], sep = "/")
-   columns = list()
-   for (idx in seq(data_paths)) {
-     # NOTE: matrices returned by h5read have to be transposed to obtain
-     # required Fortran order!
-     data <- data.frame(t(h5read(h5File, data_paths[idx])))
-     names <- t(h5read(h5File, name_paths[idx]))
-     entry <- data.frame(data)
-     colnames(entry) <- names
-     columns <- append(columns, entry)
-   }
-
-   data <- data.frame(columns)
-
-   return(data)
-   }
-
-Now you can import the ``DataFrame`` into R:
-
-.. code-block:: R
-
-   > data = loadhdf5data("transfer.hdf5")
-   > head(data)
-            first    second class
-   1 0.4170220047 0.3266449     0
-   2 0.7203244934 0.5270581     0
-   3 0.0001143748 0.8859421     1
-   4 0.3023325726 0.3572698     1
-   5 0.1467558908 0.9085352     1
-   6 0.0923385948 0.6233601     1
-
-.. note::
-   The R function lists the entire HDF5 file's contents and assembles the
-   ``data.frame`` object from all matching nodes, so use this only as a
-   starting point if you have stored multiple ``DataFrame`` objects to a
-   single HDF5 file.
-
 
 Performance
 '''''''''''

doc/source/whatsnew/v0.16.0.rst

@@ -206,7 +206,7 @@ Other enhancements
 - Added ``decimal`` option in ``to_csv`` to provide formatting for non-'.' decimal separators (:issue:`781`)
 - Added ``normalize`` option for ``Timestamp`` to normalized to midnight (:issue:`8794`)
 - Added example for ``DataFrame`` import to R using HDF5 file and ``rhdf5``
-  library. See the :ref:`documentation <io.external_compatibility>` for more
+  library. See the documentation for more
   (:issue:`9636`).
 
 .. _whatsnew_0160.api: