Thursday, May 28, 2015

Updates to the Prepare Rasters for Maxent Tool - upscaling rasters

Maxent software ( 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.

Wednesday, May 20, 2015

New tool - Duration of event for rasters for ArcGIS 10.1

I've got a new tool out for ArcMap that shows the duration of events. Events should be coded 1 and non-events coded 0. Each raster represents a distinct point in time (in my case I did an annual time step). You can download this new tool HERE.

Here is an example of the tool in practice.  We've got a vegetation mortality event that can be mapped using satellite imagery. We've done this going back over twenty years at an annual time step. Each grid cell is coded either 1 or 0. The figure on the left shows the number of times that this event has occurred. We can see that in this area the event has occurred up to five times.

Now we run the duration tool to see if the event tends be in the same place in consecutive years.The figure below left shows that only very rarely do we see three consecutive years as having an event. Mostly we see two or even just a single consecutive events.

The figure below bottom shows the ratio of the count of events to the duration of events. The values range from 1 to 4 indicating that events have re-occurred in many of these areas up to four times.

Friday, May 15, 2015

Esri removes the geoprocessing script gallery causing mayhem

Earlier this month I discovered that Esri no longer provides a link to their geoprocessing gallery.  This is disappointing to me since every time they move or discontinue something part of the user base is lost or left confused.  The following tools that I've built are affected by this change:

Topography Toolbox
Polygons to Centerlines
PRISM Data Helper
Pixel Corner Coordinates
Extract Rasters
Add Source and Batch Join Tables
Treeline Migration

Fortunately, I've ported some of the tools over to  The following tools have made the move thus far and I will be moving more soon.

Topography Toolbox
Polygons to Centerline

The following tools have been combined into the Topography Toolbox:

Riparian  Topography Toolbox
PRISM Data Helper