Monarch butterfly and milkweed models the western U.S.

Today Matt Forister and I presented the results of our habitat modeling work for monarch butterflies and milkweeds for the western U.S. I've been involved in this research now since January 2017 and am very excited about having some preliminary maps and models ready. The work is an extension of the 2015 habitat modeling effort by Madeline Steele while she was at the U.S. Fish & Wildlife Service. Our work is a collaborative effort by University of Nevada Reno, the Xerces Society, the U.S. Fish & Wildlife Service, and others. I'm excited to get to work with such an iconic species, and I hope that through conservation and societal awareness of pesticides we can halt the decline of one of the most beautiful insect species in the world.

An improved zonal statistics for dealing with overlapping buffers

A while back I posted an article about two alternative options for summarizing and extracting data from around points.  The two solutions that I posited where zonal statistics and neighborhood statistics.  Each has its advantages and disadvantages.  The standard zonal statistics tool in ArcGIS doesn't deal with overlapping polygons, which is a common problem.  The neighborhood approach tends to be slow, but has the advantage that it can deal with overlaps effectively and necessary for people doing wall-to-wall predictive maps (such as species distribution modeling).

There is, however, a third option.  The zonal statistics tool can be modified to accommodate overlaps.  That is exactly what I have done.  Below is the model that I created in Model Builder to achieve this.

I plan to have this out soon as a tool available to download.  In the mean time there are a couple of key features to this model that I'd like to point out. 

1) Iteration by Field Values - This step iterates through a categorical raster, lets say land cover classes, producing an output that represents to proportion cover for each type.

2) Intersect/Erase - Buffers are generated and the intersect and erase tools are used identify the "normal non-overlapping" portion of the buffer as well as the overlapping portion.  Unfortunately the Erase tool requires a full ArcGIS Advanced license so I'll need to put some more thought into how to make this available to folks with lower license levels.

3) Zonal statistics - The tool performs a couple of zonal statistics operations.  It sums the number of cells in each class and then sums the total number of cells to get the proportional cover.

4) Once the proportional cover has been calculated for overlapping buffer areas and non-overlapping buffer areas there is a need to put this information together.  The field calculator is used with the following formula max( !Prpn_Overlap_Raster!, !Prpn!).  This effectively deals with the fact that there are Null values from one output when there are data values from the other and visa versa.  This seems to be an effective way of getting around trying to make field mapping work.

Look soon for a new tool to automate this process.

Comments on Prepare Rasters for Maxent versus Find ArcGIS Rasters and Project to Template in MGET

On my page for the Prepare Rasters for Maxent Tool for ArcGIS I made a comment about its application versus another tool called Find ArcGIS Rasters and Project to Template in the Marine Geospatial Ecology Toolbox.  To access that page click HERE .  Here is the text of that comment:

The Marine Geospatial Ecology Tools for ArcGIS (http://mgel.env.duke.edu/mget) is an excellent toolbox that includes much of the functionality of the Prepare Rasters for Maxent toolbox. I highly recommend checking it out. In particular, check out the Find ArcGIS Rasters and Project to Template tool which will batch project and clip all rasters to a template. One primary difference between that tool and Prepare Rasters for Maxent is that Prepare Rasters for Maxent has built-in steps to resample and fill in missing data. If you know that you have gaps in your data then Prepare Rasters for Maxent may be your best bet. If you don't think that you have gaps or they are minor then consider Find ArcGIS Rasters and Project to Template as a speedier alternative. You can create a template raster by multiplying all of your rasters together in the Raster Calculator. By default this will take the intersection of all of the rasters resulting in a template that is smaller than any one of the inputs.

Updates to the Prepare Rasters for Maxent Tool - upscaling rasters

Maxent software (http://www.cs.princeton.edu/~schapire/maxent) is frequently used for presence-only species distribution modeling. Maxent requires, however, that input ASCII raster files be aligned with one another and have the same spatial extent. This tool pre-processes raster data in preparation for Maxent modeling to ensure that all rasters have the same extent, same cell size, and aren't missing data. You can download the tool HERE.

There is a new tool that can be used to upscale data. Upscaling is useful when simple resampling is insufficient. For example, if you have a 30 meter classified vegetation map simply using the majority resample to resample to 1000 meter cell size would be insufficient because it would just tell you about the majority vegetation type present. Better would be to count the number of pixels of the vegetation type of interest within the 1000 meter cells and calculate the proportion of that vegetation type. This also solves the problem of having to treat the data as categorical in Maxent. Vegetation type would have to be treated as a categorical variable whereas proportion of X vegetation type is a continuous variable.

This example illustrates the idea of upscaling.

In the image above we have a forest/non-forest GIS layer overlaid on a coarse-resolution grid. The need for the coarse resolution grid is due to uncertainty in the location of the occurrence points and the resolution of other datasets that will be used in Maxent (e.g. the MODIS satellite products have a cell size of 250 - 1000 meters depending upon the product). The image below shows tree cover at the 1000 meter scale derived from running the Upscale Rasters for Maxent Tool. An important pre-processing step is deciding which vegetation types should be included in the model and which should be omitted. Included vegetation types should be reclassified as 1 prior to running the tool and omitted vegetation types should be reclassified as 0.