.. draft (mark as complete when complete) .. model fails when adding landcover_1km.asc ======================= Using MaxEnt ======================= `MaxEnt `_ is a Java program for maximum entropy modelling of species geographic distributions, written by Steven Phillips, Miro Dudik and Rob Schapire, with support from AT&T Labs-Research, Princeton University, and the Center for Biodiversity and Conservation, American Museum of Natural History. MaxEnt Interface ----------------------- To run MaxEnt, simply click the file ``maxent.bat``. .. image:: images/maxent_overview.png :align: center :width: 450 pt * 1 - Samples panel - a list species presence location data. * 2 - Environmental layers panel - a list of ESRI ASCII raster layers that will be used for the modelling. * 3 - Advance tools - the more advance tools, output directory and other settings. To perform a model, we need a sample CSV data (the ``black_shama.csv`` in your ``samples`` directory); the environmental layers (in your ``layers`` directory) and; and output directory to save all the model results. Loading species occurrences ------------------------------ 1. To load the samples data, click the :guilabel:`Browse` button in the :guilabel:`Samples` panel. 2. A new window will appear, open your ``samples`` directory and select the ``black_shama.csv``. Click :guilabel:`Open`. .. image:: images/load_samples.png :align: center :width: 300 pt Loading environmental covariates ----------------------------------- 1. To load the raster data, click the :guilabel:`Browse` button in the :guilabel:`Environmental layers` panel. 2. A new window will appear, select your ``layers`` directory and ``Open``. .. image:: images/load_layers.png :align: center :width: 300 pt The main MaxEnt window will display the number environmental layers available in the directory. 3. Define the data type for the environmental layers. All the layers are ``Continuous`` except for ``landcover_1km`` which is a ``Categorical`` data. .. verify this one as it breaks in my own test - maning. Defining output directory ---------------------------- 1. To select the output directory, click the :guilabel:`Browse` button in the :guilabel:`Output directory` section. Select the ``output`` directory and click :guilabel:`Open`. .. image:: images/maxent_output.png :align: center :width: 300 pt Configuring Maxent features and settings ------------------------------------------- Once the species occurrences and environmental covariates are loaded, it is important to know what appropriate MaxEnt parameters and features are needed to your sample. For instance, *Copsychus cebuensis* has only 12 points of observation. Therefore, we need to find what specific feature of Maxent is best for this type of sample in order to have an accurate prediction. 1. In MaxEnt window, click :guilabel:`Help` option to view all the information about the features and settings. 2. To find what feature is appropriate for *Copsychus cebuensis*, scroll down to `Regularization and feature class` section. 3. After finding the feature, go back to MaxEnt main window by closing the `Help` window. 4. In this exercise, we will use Linear and Quadratic features. To set these features and other necessary settings, uncheck `Auto features` and select `Linear and Quadratic features`. Check `Create response curve`, `Do Jackknife` and select `Logistic` as output format for the prediction. 5. Go also to :menuselection:`Settings --> Advance` tab and set the `Maximum iterations` to ``5000`` to give time for the model to converge. In the `Experimental tab` check `Write background predictions` to obtain the values of predicted background. .. image:: images/maxent_advance.png :align: center :width: 300 pt .. image:: images/maxent_experimental.png :align: center :width: 300 pt .. Note:: * For further analysis, you can enable the Maxent to do replicates under `Basic` tab of the settings. * Threshold rule can be applied also if you want to produce a thresholded binary map. 6. Finally, close the :guilabel:`Settings` window and click :guilabel:`Run`. Running model may take some time depending on the extent, number of environmental layers and replicates. Once finished, close the MaxEnt application. Exploring MaxEnt outputs --------------------------------------- The run produces multiple output files, to immediately view the result find the html file ``Copsychus_cebuensis.html`` and open it in your web browser. .. image:: images/maxent_model_output.png :align: center :width: 450 pt .. raw:: latex \pagebreak[4]