Worked example restructured

docs/source/index.rst

@@ -21,8 +21,11 @@ Contents:
    :maxdepth: 1
 
    setup.rst
-   worked_example.rst
+   worked_example_1.rst
+   worked_example_2.rst
+   worked_example_3.rst
    biota.rst
+
 
 
 Indices and tables

docs/source/setup.rst

@@ -4,4 +4,52 @@ Setup instructions
 Requirements
 ------------
 
-To complete
+The ``biota`` module is written for Python in Linux. It should be possible to run on most Desktop PCs or a Linux server.
+
+Installing Anaconda Python
+--------------------------
+
+We recommend running the ``biota`` module in Anaconda Python.
+
+To install Anaconda Python, open a terminal window, change directory to the location you'd like to install Anaconda Python, and run the following commands:
+
+.. code-block:: console
+    
+    wget https://repo.continuum.io/archive/Anaconda2-4.2.0-Linux-x86_64.sh
+    bash Anaconda2-4.2.0-Linux-x86_64.sh
+
+    
+Once complete, you'll need to add this version of Python to your .bashrc file as follows:
+
+.. code-block:: console
+    
+    # Substitute root for the path to your system's installation and .bashrc file.
+    echo 'export PATH="~/anaconda2/bin:$PATH"' >> ~/.bashrc
+    exec -l $SHELL
+
+
+If this has functioned, on executing ``python`` in a terminal window, you should ssee the following:
+
+.. code-block:: console
+
+    Python 2.7.12 |Anaconda custom (64-bit)| (default, Jul  2 2016, 17:42:40) 
+    [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
+    Type "help", "copyright", "credits" or "license" for more information.
+    Anaconda is brought to you by Continuum Analytics.
+    Please check out: http://continuum.io/thanks and https://anaconda.org
+    >>> 
+
+Installing biota
+----------------
+
+To install ``biota``, enter the following in a terminal window:
+
+.. code-block:: console
+    
+    pip install git+https://bitbucket.org/sambowers/biota
+
+If successful, you should now be able to import ``biota`` in Python:
+
+.. code-block:: python
+    
+    import biota

docs/source/worked_example_1.rst

@@ -0,0 +1,19 @@
+Worked example: part 1
+======================
+
+In this worked example we'll run through an example based on an area of Southeastern Tanzania called Kilwa District (Fig). This is a location where the University of Edinburgh coordinates a network of forest plots where we have good data on aboveground biomass.
+
+In this section we'll use ``biota`` to download ALOS mosaic data for the Kilwa region.
+
+Downloading data
+----------------
+
+[To follow]
+
+In short
+--------
+
+The download script is stored in ``biota/download.py``, and has a command line interface. The ``biota`` tool is at present limited to using the ``--large`` 5x5 degree tiles, but will shortly be shifted to use 1x1 degree tiles.
+
+Kilwa District is found in the large tile 35 longitude, -5 latitude.
+

docs/source/worked_example.rst → docs/source/worked_example_2.rst

@@ -1,15 +1,7 @@
+Worked example: part 2
+======================
 
-
-
-Here we'll run through an example based on an area of Southeastern Tanzania called Kilwa District (Fig). This is a location where the University of Edinburgh coordinates a network of forest plots where we have good data on aboveground biomass.
-
-We'll download data, generate maps of gamma0 backscatter, AGB and forest cover.
-
-
-Downloading data
-----------------
-
-[To follow]
+In this section we'll use ``biota`` to generate maps of gamma0 backscatter, AGB, and forest cover.
 
 Open Python and import biota
 ----------------------------

docs/source/worked_example_3.rst

@@ -0,0 +1,6 @@
+Worked example: part 3
+======================
+
+In this section we'll use ``biota`` to generate change maps based on comparisons of AGB estimates.
+
+To follow