Updating the website

deforisk_plugin_dialog_base.ui

@@ -579,7 +579,7 @@
        <item row="3" column="1">
         <widget class="QLineEdit" name="mcmc">
          <property name="text">
-          <string>5000</string>
+          <string>1000</string>
          </property>
          <property name="placeholderText">
           <string>5000</string>

help/docsrc/get_started.org

@@ -11,12 +11,32 @@
 
 * Introduction
 
-To test the plugin installation and have a first look at its functionalities, try it on a small area of interest (AOI) such as the [[https://en.wikipedia.org/wiki/Martinique][Martinique]] island (1128 km^{2}) which as the MTQ iso code. Testing the plugin on a small AOI has the advantage of making computations faster so that you can directly see the outputs, interpret the results, and understand the functioning of the plugin.
+#+begin_export rst
+.. |ico_py| image:: _static/icon_python_console_toolbar.png
+   :class: no-scaled-link
+.. |ico_deforisk| image:: _static/icon_deforisk_toolbar.png
+   :class: no-scaled-link   
+#+end_export
+
+Open QGIS on your computer. To have access to log messages, activate the "Log Messages" panel in QGIS going to =View > Panel > Log Messages= in the Menu. When using a plugin, it is also a good habit to open the Python console in QGIS to have access to Python messages returned in the console. To open it, click on the Python icon @@rst:|ico_py|@@ in the "Plugins Toolbar". If the toolbar is not visible, activate it going to =View > Toolbars > Plugins Toolbar= in the Menu.
+
+Once the plugin has been installed (see [[file:installation.html][Installation]] instructions), open the plugin clicking on its icon @@rst:|ico_deforisk|@@. You should see the versions of the dependencies installed in your environment written in the Python console. Check that these version numbers correspond to the last version for each dependency. Otherwise upgrade your dependencies.
+
+#+begin_src python :results none :exports code
+osmconvert 0.8.10
+osmfilter 1.4.4
+geefcc 0.1.3
+pywdpa 0.1.6
+forestatrisk 1.2
+riskmapjnr 1.3
+#+end_src
+
+To test the plugin and have a first look at its functionalities, try it on a small area of interest (AOI) such as the [[https://en.wikipedia.org/wiki/Martinique][Martinique]] island (1128 km^{2}) which has the MTQ iso code. Testing the plugin on a small AOI has the advantage of making computations fast so that you can directly see the outputs, interpret the results, and understand the functioning of the plugin.
 
 * Get variables
 
 #+attr_rst: :alt MTQ variables
-[[file:_static/interface_MTQ-tuto.png]]
+[[file:_static/interface_MTQ-tuto-variables.png]]
 
 - ~Working directory~: Select your working directory. Here ~/home/<username>/deforisk/MTQ-tuto~, but it could be ~C:\Users\<username>\deforisk\MTQ-tuto~ on Windows for example.
 - ~Area Of Interest~: MTQ
@@ -29,13 +49,35 @@ To test the plugin installation and have a first look at its functionalities, tr
 - ~WDPA access~: Personal WDPA API Token or path to text file with WDPA_KEY environmental variable.
 - ~Projection EPSG code~: EPSG:5490
 
-Click the run button and you should get the following layer on QGIS:
+Click the run button. A forest cover change map appears in the list of QGIS layers (see image below and click to enlarge) and a plot of the forest cover change ~fcc123.png~ is created in folder ~outputs/variables~. New folders are created in the working directory among which the ~data_raw~ folder which includes raw data with intermediary files and the ~data~ folder which includes processed data used for models and plots. You can visualize the road network for example adding the ~roads_proj.shp~ vector file, which is located in the ~data_raw~ directory, in QGIS.
 
 #+attr_rst: :width 650px :alt QGIS variables
-[[file:_static/qgis-variables.png]]
+[[file:_static/qgis-variables-results.png]]
 
 * Benchmark model
 
+#+attr_rst: :alt MTQ variables
+[[file:_static/interface_MTQ-tuto-benchmark.png]]
+
+** Fit model to data
+
+- ~Deforestation threshold (%)~: 99.5%
+- ~Max. distance to forest edge (m)~: 2500
+- ~calib. period~: Checked, the model is fitted over the calibration period (t1--t2).
+- ~hist. period~: Checked, the model is fitted over the historical period (t1--t3).
+
+Click the ~Run~ button to estimate the deforestation risk with the benchmark model and predict the deforestation risk at t1 using both data on the calibration and historical periods. Maps with classes of deforestation risk are added to the list of QGIS layers (see image below) and new folders with results are created in the ~outputs/rmj_benchmark/~ directory including the ~<period>/defrate_cat_bm_<period>.csv~ tables with deforestation rates for each class of deforestation risk (see details [[file:plugin_api.html#defrate-table][here]]).
+
+#+attr_rst: :width 650px :alt QGIS variables
+[[file:_static/qgis-benchmark-results.png]]
+
+** Predict the deforestation risk
+
+- ~t2 validation~: Checked, computes predictions at t2 for validation (using the benchmark model fitted over the calibration period).
+- ~t3 forecast~: Checked, computes predictions at t3 for forecasting (using the benchmark model fitted over the historical period).
+
+Click the ~Run~ button to predict the deforestation risk at t2 and t3 using the benchmark model. Maps with classes of deforestation risk are added to the list of QGIS layers (see image below) and new folders with results are created in the ~outputs/rmj_benchmark/~ directory.
+
 * Forestatrisk models
 
 * Moving window models

help/docsrc/get_started.rst

@@ -11,12 +11,30 @@ Get started
 Introduction
 ------------
 
-To test the plugin installation and have a first look at its functionalities, try it on a small area of interest (AOI) such as the `Martinique <https://en.wikipedia.org/wiki/Martinique>`_ island (1128 km\ :sup:`2`\) which as the MTQ iso code. Testing the plugin on a small AOI has the advantage of making computations faster so that you can directly see the outputs, interpret the results, and understand the functioning of the plugin.
+.. |ico_py| image:: _static/icon_python_console_toolbar.png
+   :class: no-scaled-link
+.. |ico_deforisk| image:: _static/icon_deforisk_toolbar.png
+   :class: no-scaled-link   
+
+Open QGIS on your computer. To have access to log messages, activate the “Log Messages” panel in QGIS going to ``View > Panel > Log Messages`` in the Menu. When using a plugin, it is also a good habit to open the Python console in QGIS to have access to Python messages returned in the console. To open it, click on the Python icon |ico_py| in the “Plugins Toolbar”. If the toolbar is not visible, activate it going to ``View > Toolbars > Plugins Toolbar`` in the Menu.
+
+Once the plugin has been installed (see `Installation <installation.html>`_ instructions), open the plugin clicking on its icon |ico_deforisk|. You should see the versions of the dependencies installed in your environment written in the Python console. Check that these version numbers correspond to the last version for each dependency. Otherwise upgrade your dependencies.
+
+.. code:: python
+
+    osmconvert 0.8.10
+    osmfilter 1.4.4
+    geefcc 0.1.3
+    pywdpa 0.1.6
+    forestatrisk 1.2
+    riskmapjnr 1.3
+
+To test the plugin and have a first look at its functionalities, try it on a small area of interest (AOI) such as the `Martinique <https://en.wikipedia.org/wiki/Martinique>`_ island (1128 km\ :sup:`2`\) which has the MTQ iso code. Testing the plugin on a small AOI has the advantage of making computations fast so that you can directly see the outputs, interpret the results, and understand the functioning of the plugin.
 
 Get variables
 -------------
 
-.. image:: _static/interface_MTQ-tuto.png
+.. image:: _static/interface_MTQ-tuto-variables.png
     :alt: MTQ variables
 
 - ``Working directory``: Select your working directory. Here ``/home/<username>/deforisk/MTQ-tuto``, but it could be ``C:\Users\<username>\deforisk\MTQ-tuto`` on Windows for example.
@@ -39,15 +57,44 @@ Get variables
 
 - ``Projection EPSG code``: EPSG:5490
 
-Click the run button and you should get the following layer on QGIS:
+Click the run button. A forest cover change map appears in the list of QGIS layers (see image below and click to enlarge) and a plot of the forest cover change ``fcc123.png`` is created in folder ``outputs/variables``. New folders are created in the working directory among which the ``data_raw`` folder which includes raw data with intermediary files and the ``data`` folder which includes processed data used for models and plots. You can visualize the road network for example adding the ``roads_proj.shp`` vector file, which is located in the ``data_raw`` directory, in QGIS.
 
-.. image:: _static/qgis-variables.png
+.. image:: _static/qgis-variables-results.png
     :width: 650px
     :alt: QGIS variables
 
 Benchmark model
 ---------------
 
+.. image:: _static/interface_MTQ-tuto-benchmark.png
+    :alt: MTQ variables
+
+Fit model to data
+~~~~~~~~~~~~~~~~~
+
+- ``Deforestation threshold (%)``: 99.5%
+
+- ``Max. distance to forest edge (m)``: 2500
+
+- ``calib. period``: Checked, the model is fitted over the calibration period (t1--t2).
+
+- ``hist. period``: Checked, the model is fitted over the historical period (t1--t3).
+
+Click the ``Run`` button to estimate the deforestation risk with the benchmark model and predict the deforestation risk at t1 using both data on the calibration and historical periods. Maps with classes of deforestation risk are added to the list of QGIS layers (see image below) and new folders with results are created in the ``outputs/rmj_benchmark/`` directory including the ``<period>/defrate_cat_bm_<period>.csv`` tables with deforestation rates for each class of deforestation risk (see details `here <plugin_api.html#defrate-table>`_).
+
+.. image:: _static/qgis-benchmark-results.png
+    :width: 650px
+    :alt: QGIS variables
+
+Predict the deforestation risk
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- ``t2 validation``: Checked, computes predictions at t2 for validation (using the benchmark model fitted over the calibration period).
+
+- ``t3 forecast``: Checked, computes predictions at t3 for forecasting (using the benchmark model fitted over the historical period).
+
+Click the ``Run`` button to predict the deforestation risk at t2 and t3 using the benchmark model. Maps with classes of deforestation risk are added to the list of QGIS layers (see image below) and new folders with results are created in the ``outputs/rmj_benchmark/`` directory.
+
 Forestatrisk models
 -------------------
 

help/docsrc/installation.org

@@ -23,9 +23,9 @@ To be able to use the ~deforisk~ QGIS plugin, you need to activate the developer
 - Toggle the Developer Mode setting, at the top of the "For developers" page.
 - Read the disclaimer for the setting you choose. Click "Yes" to accept the change.
 
-** Install Qgis and GDAL on Windows
+** Install QGIS and GDAL on Windows
 
-To install Qgis and GDAL on Windows, use the [[https://trac.osgeo.org/osgeo4w/][OSGeo4W]] network installer. OSGeo4W is a binary distribution of a broad set of open source geospatial software for Windows environments (Windows 11 down to 7). Select /Express Install/ and install both Qgis and GDAL. Several Gb of space will be needed on disk to install these programs. This will also install /OSGeo4W Shell/ to execute command lines.
+To install QGIS and GDAL on Windows, use the [[https://trac.osgeo.org/osgeo4w/][OSGeo4W]] network installer. OSGeo4W is a binary distribution of a broad set of open source geospatial software for Windows environments (Windows 11 down to 7). Select /Express Install/ and install both QGIS and GDAL. Several Gb of space will be needed on disk to install these programs. This will also install /OSGeo4W Shell/ to execute command lines.
 
 ** Install the ~forestatrisk~ and ~riskmapjnr~ Python packages on Windows
 
@@ -44,9 +44,9 @@ python3.exe --version
 
 * On Unix-like systems (Linux and macOS)
 
-** Install Qgis and GDAL on Unix-like systems
+** Install QGIS and GDAL on Unix-like systems
 
-Install Qgis and GDAL on your system, for example using ~apt-get~ for Debian/Ubuntu Linux distributions.
+Install QGIS and GDAL on your system, for example using ~apt-get~ for Debian/Ubuntu Linux distributions.
 
 #+begin_src shell
 sudo apt-get update
@@ -70,7 +70,7 @@ python3 -m pip install forestatrisk riskmapjnr gdal==$(gdal-config --version)
 deactivate
 #+end_src
 
-Then, in the ~startup.py~ [[https://docs.qgis.org/3.4/en/docs/pyqgis_developer_cookbook/intro.html#running-python-code-when-qgis-starts][Python file]], add the following two lines, adapting the path to your specific case (check the Python version). These two lines will be executed when Qgis starts and will add the path to the packages installed in the virtual environment to ~sys.path~.
+Then, in the ~startup.py~ [[https://docs.qgis.org/3.4/en/docs/pyqgis_developer_cookbook/intro.html#running-python-code-when-qgis-starts][Python file]], add the following two lines, adapting the path to your specific case (check the Python version). These two lines will be executed when QGIS starts and will add the path to the packages installed in the virtual environment to ~sys.path~.
 
 #+begin_src python :results output :exports both
 import sys
@@ -99,9 +99,9 @@ In the ~deforisk~ plugin, for the ~WDPA access~ argument available in the "Get v
 #+attr_rst: :width 500px :alt WDPA access
 [[file:_static/wdpa_access.png]]
 
-* Installing the ~deforisk~ plugin in Qgis
+* Installing the ~deforisk~ plugin in QGIS
 
 - Download the ~deforisk~ [[https://github.com/ghislainv/deforisk-qgis-plugin/archive/refs/heads/main.zip][zip file]] from GitHub.
-- Open Qgis.
-- In Qgis menu bar, go to ~Extensions/Install extensions/Install from ZIP~.
+- Open QGIS.
+- In QGIS menu bar, go to ~Extensions/Install extensions/Install from ZIP~.
 - Select the zip file that has been downloaded.

help/docsrc/installation.rst

@@ -26,10 +26,10 @@ To be able to use the ``deforisk`` QGIS plugin, you need to activate the develop
 
 - Read the disclaimer for the setting you choose. Click “Yes” to accept the change.
 
-Install Qgis and GDAL on Windows
+Install QGIS and GDAL on Windows
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-To install Qgis and GDAL on Windows, use the `OSGeo4W <https://trac.osgeo.org/osgeo4w/>`_ network installer. OSGeo4W is a binary distribution of a broad set of open source geospatial software for Windows environments (Windows 11 down to 7). Select *Express Install* and install both Qgis and GDAL. Several Gb of space will be needed on disk to install these programs. This will also install *OSGeo4W Shell* to execute command lines.
+To install QGIS and GDAL on Windows, use the `OSGeo4W <https://trac.osgeo.org/osgeo4w/>`_ network installer. OSGeo4W is a binary distribution of a broad set of open source geospatial software for Windows environments (Windows 11 down to 7). Select *Express Install* and install both QGIS and GDAL. Several Gb of space will be needed on disk to install these programs. This will also install *OSGeo4W Shell* to execute command lines.
 
 Install the ``forestatrisk`` and ``riskmapjnr`` Python packages on Windows
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -50,10 +50,10 @@ Note: In case of problems, you can check the version of Python used by OSGeo4W u
 On Unix-like systems (Linux and macOS)
 --------------------------------------
 
-Install Qgis and GDAL on Unix-like systems
+Install QGIS and GDAL on Unix-like systems
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Install Qgis and GDAL on your system, for example using ``apt-get`` for Debian/Ubuntu Linux distributions.
+Install QGIS and GDAL on your system, for example using ``apt-get`` for Debian/Ubuntu Linux distributions.
 
 .. code:: shell
 
@@ -79,7 +79,7 @@ On recent systems, you cannot use pip to install Python packages system-wide. As
     python3 -m pip install forestatrisk riskmapjnr gdal==$(gdal-config --version)
     deactivate
 
-Then, in the ``startup.py`` `Python file <https://docs.qgis.org/3.4/en/docs/pyqgis_developer_cookbook/intro.html#running-python-code-when-qgis-starts>`_, add the following two lines, adapting the path to your specific case (check the Python version). These two lines will be executed when Qgis starts and will add the path to the packages installed in the virtual environment to ``sys.path``.
+Then, in the ``startup.py`` `Python file <https://docs.qgis.org/3.4/en/docs/pyqgis_developer_cookbook/intro.html#running-python-code-when-qgis-starts>`_, add the following two lines, adapting the path to your specific case (check the Python version). These two lines will be executed when QGIS starts and will add the path to the packages installed in the virtual environment to ``sys.path``.
 
 .. code:: python
 
@@ -113,13 +113,13 @@ In the ``deforisk`` plugin, for the ``WDPA access`` argument available in the 
     :width: 500px
     :alt: WDPA access
 
-Installing the ``deforisk`` plugin in Qgis
+Installing the ``deforisk`` plugin in QGIS
 ------------------------------------------
 
 - Download the ``deforisk`` `zip file <https://github.com/ghislainv/deforisk-qgis-plugin/archive/refs/heads/main.zip>`_ from GitHub.
 
-- Open Qgis.
+- Open QGIS.
 
-- In Qgis menu bar, go to ``Extensions/Install extensions/Install from ZIP``.
+- In QGIS menu bar, go to ``Extensions/Install extensions/Install from ZIP``.
 
 - Select the zip file that has been downloaded.