Add basic installation, README.rst in index page and minor fixes

README.rst

@@ -0,0 +1,22 @@
+phys2denoise: A toolbox for physiological metrics calculation
+=============================================================
+
+This package is designed for use in the metrics calculation of physiological data, more specifically of cardiac and respiratory signals, to be used in fMRI denoising.
+
+
+.. image:: https://readthedocs.org/projects/phys2denoise/badge/?version=latest
+   :target: http://phys2denoise.readthedocs.io/en/latest
+.. image:: https://img.shields.io/badge/license-Apache%202-blue.svg
+   :target: http://www.apache.org/licenses/LICENSE-2.0
+.. image:: https://img.shields.io/badge/python-3.6+-blue.svg
+   :target: https://www.python.org/downloads/
+
+
+.. _licensing:
+
+License Information
+-------------------
+
+This codebase is licensed under the Apache License, Version 2.0. The full
+license can be found in the `LICENSE <https://github.com/physiopy/phys2denoise/blob/master/LICENSE>`_ file in the ``phys2denoise`` distribution. You may also
+obtain a copy of the license at: http://www.apache.org/licenses/LICENSE-2.0.

docs/index.rst

@@ -1,3 +1,4 @@
+.. include:: ../README.rst
 
 Contents
 --------

docs/installation.rst

@@ -5,6 +5,17 @@ Installation and setup
 
 .. _basic_installation:
 
+Basic installation
+------------------
+
+The easiest way to install ``phys2denoise`` is to use ``pip``. Assuming you have
+Python >= 3.6 installed, you can install ``phys2denoise`` by opening a terminal
+and running the following:
+
+.. code-block:: bash
+
+   pip install phys2denoise
+
 Developer installation
 --------------------
 

docs/user_guide/exporting.rst

@@ -10,7 +10,8 @@ This can be done using the :py:func:`export_metric` function, which provides the
 - Defining the output file extension and file prefix.
 - Defining the number of timepoints to be considered.
 
-The following example shows how to export the computed respiratory variance time using a Physio object.
+The following example shows how to export the computed respiratory variance time using a Physio object. In the following example,
+we consider that the Physio object is ``resp``, containing the respiratory data, peaks and troughs.
 
 .. code-block:: python
 

docs/user_guide/metrics.rst

@@ -64,7 +64,7 @@ For further information refer to the :py:mod:`physutils` documentation.
 Without using a Physio object
 #############################
 
-However, if the use of :py:mod:`physutils` is not preferred, the metrics can be also computed without it. The following
+However, if the use of the ``Physio`` object of the :py:mod:`physutils` module is not preferred, the metrics can be also computed without it. The following
 example shows how to compute the heart rate and the heart rate variability using the :py:mod:`phys2denoise` package.
 
 .. code-block:: python
@@ -73,4 +73,4 @@ example shows how to compute the heart rate and the heart rate variability using
 
     # Given that the respiratory signal is stored in `data`, the peaks in `peaks`, the troughs in `troughs`
     # and the sample rate in `sample_rate`
-    _, rvt = respiratory_variance_time(physio, peaks, troughs, sample_rate)
+    _, rvt = respiratory_variance_time(data, peaks, troughs, sample_rate)