Environmental Layers for HPC Maximum Entropy Species Distribution Models in Great Smoky Mountains National Park
Currently there are 10 environmental layers that were used by Simmerman et. al in the demonstration project, “Exploring similarities among many species distributions.”
- Bedrock geology
- Digital elevation model
- Slope measured in degrees
- Solar radiation data
- Soil organic type
- Terrain shape index
- Topographic convergence index
- Leaf on canopy cover
- Understory density classes
- Vegetation classes
The contribution of environmental variables to each “Maximum Entropy” Species Distribution Model (MaxEnt SDM) environmental variables are accessible from each model under the “Environmental Layers” tab.
The help icon accompanying each model provides this text:
This is a species distribution model (SDM) produced by MaxEnt. This SDM is actually a composite from ten cross-validation runs for each species (see cross-validation results tab for more information). Original ATBI record locations are shown with black dots. The color scale goes from 0 probability of presence (dark brown) to 100% probability (dark green).
Below is a screen capture of the model generated for the Fraser fir (Abies fraseri). This model is based on 474 occurrence records. The full size image is available online at <http://seelab.eecs.utk.edu/alltaxa/maps/Abies_fraseri.png>
Interestingly, the MaxEnt model output suggests that the “Digital Elevation Model” contributed 88.8% to the Species Distribution Model for Abies frasieri. This makes sense, since the Fraser fir is a species of conifer favoring cold environments that inhabits only the highest elevations of the Park. The remaining layers contribute less than 5% to the model.
I’m copying out the taxonomic classification from Wikipedia:
The purpose is to access the records from the ATBI database, where I don’t see the Fraser fir listed in the ATBI “plants” kingdom. From <http://tremont22.campus.utk.edu/ATBI_Query.cfm> I searched by “order’ for “pinales.”
Fraser fir is accessible: <http://tremont22.campus.utk.edu/ATBI_Species.cfm?genus=Abies&epithet=fraseri&subspecies=%7E>. Interestingly, the number of specimens in the database is 866. Contrast this with the 474 records that were used to generate the model. The model may simply be older (there does not appear to be a timestamp for the model; either from “Get Info” or opening up “Properties” in GIMP for both the large 299×1302 pixel PNG file and the small 600×269 pixel png) or, not all 866 occurrence records have spatial coordinates associated (e.g., they are “references from the literature.”)
Posted on February 24, 2014, in Practicum, Research, Uncategorized and tagged Categorical Variables, Continuous Variables, Maximum Entropy, Species Distribution Modeling. Bookmark the permalink. Leave a comment.