New tool - Create Available Points Toolbox for ArcGIS

I have a new tool out that can be used to generate background/available points for habitat modeling (resource selection functions) in ArcMap.  It should work in ArcGIS Pro as well since it is entirely built within ModelBuilder and doesn't rely on any python. The user provides 1) their used points (e.g. occurrences), 2) a buffer from which available points can be selected, and 3) the ratio of used to available points. The tool will also combine multiple files into a single file using the filename to differentiate. This tool would be useful to wildlife biologists and others who work with radio-collar data and want a simple tool that runs in GIS. You can download the tool at https://www.arcgis.com/home/item.html?id=f5515ef257774ed790b9b64cf5d50fc5.
 

New paper - Host Plants and Climate Structure Habitat Associations of the Western Monarch Butterfly

Matt Forister, myself, and our collaborators at the Xerces Society and the USFWS have a new paper out titled "Host Plants and Climate Structure Habitat Associations of the Western Monarch Butterfly" which is published in the journal Frontiers in Ecology and Evolution. In this paper we model the habitat associations between monarch butterfly, their milkweed host plants, and a number of climatic, topographic, land use, and soil variables. We also perform habitat modeling for 13 of the most common milkweed species in the western U.S. Our study is the first large-scale habitat modeling study focused on the western population of the monarch butterfly which overwinters on the California coast and migrates inland towards the Rocky Mountains. Our paper is open access meaning that anyone can read and download it. You can go to it by clicking HERE.

To facilitate this kind of modeling we used an online citizen-science mapping tool called the Western Monarch and Milkweed Mapper. You can use the WMMM to upload your photos of monarchs and milkweeds in order to help us build better models in the future!  The WMMM also flags recent monarch sightings so that you can see when the monarchs are arriving in your area.  The WMMM also has great resources for learning how to identify the different species of milkweeds.  You can access the Western Monarch and Milkweed Mapper by clicking HERE.

Our habitat modeling work was also made possible by the tremendous amount of legwork by Madeline Steele and Joe Engler (USFWS) who completed a first version of these habitat models in 2016. Most of the variables that we used were originally compiled by Madeline, and the methods that we used followed Madeline's approach.

Finally, we should note that we have made high-resolution maps as well as details about the methodology available in the supplementary material. I would encourage you to check out these resources. For GIS users we have GeoTIFF versions of our maps available. Please contact me and I will send you a link to these files.

Citation: Dilts, T.E., Steele, M.O., Engler, J.D., Pelton, E.M., Jepsen, S.J., McKnight, S.J., Taylor, A.R., Fallon, C.E., Black, S.H., Cruz, E.E., Craver, D.R., & Forister, M.L. (2019) Host plants and climate structure habitat associations of the western monarch butterfly. Frontiers in Ecology and Evolution, 7, 188.

Adoption of monarch models by the Western Association of Fish & Wildlife Agencies

Great news.  The Western Association of Fish & Wildlife Agencies is now adopting our maps as part of the basis of their Draft Monarch Butterfly Conservation Management Plan. It is great to see western states taking the decline of this iconic species seriously and starting down the path of planning to help ensure their long-term survival.  You can view their news release by clicking HERE.

I'm excited to announce that our draft manuscript is underway and that we expect submission soon.

Paper assigned to an issue - Contrasting climate niches among co‐occurring subdominant forbs of the sagebrush steppe

Our paper "Contrasting climate niches among co‐occurring subdominant forbs of the sagebrush steppe" has been assigned to an issue in Diversity and Distributions. It will be Barga, S.C., Dilts, T.E., & Leger, E.A. (2018) Contrasting climate niches among co‐occurring subdominant forbs of the sagebrush steppe. Diversity and Distributions, 24(9): 1291-1307. Good work Sarah!

New paper - Contrasting climate niches among co-occurring sub-dominant forbs of the sagebrush steppe

Sarah Barga, Beth Leger, and myself just got a paper accepted in Diversity and Distributions!  It is titled "Contrasting climate niches among co-occurring sub-dominant forbs of the sagebrush steppe". The paper projects species distribution models for ten sub-dominant herbaceous forbs in the Great Basin. We then looked at niche overlap and found very little between the ten species. There was no relationship between phylogentic distance and niche overlap. We also looked at how species responded to temperature and precipitation variability and found that there were differences among different life forms. We hope that our paper findings will help conservationists understand which species may be more or less suitable to climatic variability.

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.

Upcoming Great Basin LCC Webinar on Pygmy Rabbit

Marjorie Matocq is presenting next Monday for the Great Basin Landscape Conservation Cooperative webinar series.  Sign up at http://greatbasinlcc.org/webinar-series .  If you can't make it there will be a recorded seminar available on YouTube in a couple of weeks.

Sarah Barga wins 2nd place in GSA poster contest

It is always great news when students win awards!  Recently Sarah Barga, an EECB Ph.D. student advised by Beth Leger, won 2nd place in UNR's Graduate Student Association student poster contest for her poster entitled "Creating maps of potential habitat for Great Basin forbs using herbarium data". I'm proud to say that I helped her get started with the Maxent modeling, but really, Sarah has done a tremendous amount of interesting work and is currently working on finalizing two manuscripts at the same time.  The maps on the right are straight off of her poster. The different colors correspond with the amount of overlap for different top models. You can view her poster by clicking HERE and her research by visiting her website HERE .

Paper is available online - Multi-scale connectivity and graph theory highlight critical areas for conservation under climate change

Our paper "Multi-scale connectivity and graph theory highlight critical areas for conservation under climate change" is now available online HERE .

In this paper we use a combination of circuit theory and graph theory to assess changes to Mohave ground squirrel from proposed solar and wind energy development. Graph theory is used to assess both overall changes in habitat connectivity and to map out core areas and stepping stones that may be important for dispersal.

Current citation:

Dilts, T. E., Weisberg, P. J., Leitner, P., Matocq, M. D., Inman, R. D., Nussear, K. E. and Esque, T. C. (2016), Multi-scale connectivity and graph theory highlight critical areas for conservation under climate change. Ecological Applications. Accepted Author Manuscript. doi:10.1890/15-0925

New tool - Generate points around points aka generate background points or available points

Habitat modeling techniques, such as conditional logistic regression, require a random sample of background points used to quantify available habitat. One common assumption of resource selection functions is that animals have an equal probability of using background points as they do occurrence points. For animals that move across the landscape this assumption is often violated if the entire movement corridor is considered as background. This tool alleviates this concern by creating a local sample of background points around known occurrence points. There are two versions of this tool. The large version is recommended for most applications as it tiles the data resulting in faster processing times. It does this by using a parameter specifying the number of features per tile and then tiling (splitting) the dataset. The smaller datasets result in much faster run times and the results are appended to an empty output shapefile continuously.  If there is a power outage or some other interruption it should be possible to go back and determine how much of the dataset got processed and which points got processed.

The map on the left shows the original occurrence points as white dots and 10 random points around each occurrence as small black points. The new tool is available HERE . Other GIS tools are available as always from the download page on our lab's website HERE

Common question - How to combine raster and vector data and deal with NoData

This one is probably the most common question I get.  It goes something along the line of  "I've got some polygon/line data that I want to combine with a raster layer, but how do I deal with the NoData outside the polygon?". Other situations that this apply to include other raster outputs that use NoData as their background, such as outputs from Brownian Bridges, or remote sensing images in which part of the image may be masked. Hence, nearly everyone who works with ArcMap in a natural resource context is likely to encounter this problem at least once (if not nearly daily in my case).

Here is a hypothetical example and solution. In the picture to the right we've got a habitat model (raster) and buffered roads which are not suitable habitat for our hypothetical species. We wish to combine the two layers to yield a habitat model in which all areas near roads are not suitable habitat (value = 0).

In ArcGIS the first step would be to convert the polygon to raster. We might do this using the Polygon to Raster Tool.  It doesn't matter what the Value Field is set to but you probably want to set the Cellsize to the same as the habitat model layer (see the picture to the right).

Then use the IsNull tool  to convert all areas that are NoData to 1.  The IsNull tool is in the Spatial Analyst toolbox and is also available as Map Algebra in the Raster Calculator tool. IsNull is a really simple, but also one of the most powerful tools in ArcMap.

The final step involves the use of the Con tool in Spatial Analyst to combine the IsNull output with the original raster (see below). The input conditional raster should be the output from the IsNull tool. The expression selects all cells with a value of 0 (i.e. in this case they are within the road buffer). The true value is set to 0 to indicate that areas near roads are unsuitable habitat. The false value uses the original habitat suitability raster to indicate that for area not near roads the habitat is the same as the habitat model.

The final result  is map that looks like the one below. Areas near roads all have a value set to zero. You can also combine IsNull and Con in raster calculator using the following type of statement: Con(IsNull[Raster],0,[Raster]) or use ModelBuilder to streamline the process.