Obtaining KDE values from ArcMET

[Malle Carrasco-Harris]

Hi Colin,

I've read many of the posts on here and am glad for the assistance! This is my first semester of using GIS and I love it and find it very rewarding to see the data me and my volunteers worked so hard to collect finally appear. However, like many new users, I'm having some issues I was hoping someone could help me on.

I've created a map with kde's for snake locations. My point feature class included 13 different snakes, and the ArcMET kde tool was able to create individual kde's for those individual animals. Now, I'd like to look at what the 50% and 95% values kde utilization distribution numbers are so I can compare them to previously recorded results, but am stumbling there. It seems that the way most other tools do this is by having individual point feature classes for each animal and then doing percent contours (if I'm remembering correctly) and looking at the area within. I think there may be a way to do this in GME through looping, but that's out of my league when it comes to my script and R.

Could you help me take my kde rasters and decipher a meaningful UD number?. This will really help in the future since I will be collecting data for more animals.


All the best,

Malle

[GIS in Ecology]

I apologize, I recently posted a new post and did not include some information.

I'm running ArcGIS v3 on a Mac that's running Windows 7 on Parallel.

I've collected copperhead spatial data for my Ph.D. dissertation.

Best,

Malle

[GIS in Ecology]

Hi Malle,

 

Thanks for your post.

 

By the sounds of it, you're facing two issues. The first is to separate your data set into the data layers for each individual, and the second is to then calculate the 50% and 95% percentage volume contours (PVCs)  for each individual from the KDEs you've generated using ArcMET.

 

For the first issue, there's a tool in GME which will allow you to separate our a data layer into new data layers based on the values in a specific field in it's attribute table. Alternatively, you should be able to use the SPLIT tool in ArcGIS (see http://pro.arcgis.com/en/pro-app/tool-reference/analysis/split.htm for more information).

 

In terms of generating the 50% and 95% PVCs from your KDEs, once you have your data layer divided up so that you have the individual point data layers for each individual, then there is also a tool in GME for doing this (although a few people have had problems with it), or you can use the free tools that I've put together for doing this, which you can download from here:  http://www.gisinecology.com/Home_Range_Tools.zip. More information about this is posted below.

 

I hope this helps, and if I've mis-interpreted what you are asking about, or if you have nay further problems, just post back on this thread.

 

All the best,

 

Colin

 

Home Range Tools from GIS In Ecology:

 

As a result of discussions during a recent course, I finally sat down and put together a custom toolbox for ArcGIS users for automatically running home range analyses. These tools are based on the processes first outlined on this thread, and later fleshed out in An Introduction To Using GIS in Marine Biology: Supplementary Workbook Four - Investigating The Home Ranges Of Individual Animals. This includes the ability to create kernel density estimates (KDE) in environments with barriers to movements. Currently, there are few other ways of doing this, and none that I know of which allow you to take into account complex barriers to movements (such as coastlines). These tools can be used  with both marine and terrestrial data sets.

 

In addition, it provides tools for extracting percentage volume contours (PVCs) from KDEs using the approach I developed for Supplementary Workbook Four, as well as tools to allow you to generate multiple 95% PVCs from KDEs from the same data set each with a different h value (also known as the smoothing parameter, bandwidth or search radius) to help with selecting the optimal value for this using the ad hoc approach from Kie 2013 (Animal Telemetry 1: 13), which you can download from here http://www.animalbiotelemetry.com/content/pdf/2050-3385-1-13.pdf, which is the approach I recommend for doing this.

 

If you are interested in using this toolbox, you can download it from: http://www.gisinecology.com/Home_Range_Tools.zip. There's a Readme file in the compressed folder which provides information about how to install it on your computer and how to import it into your version of ArcGIS. This toolbox is free to use, customise and distribute (although you will need the usual ArcGIS licences to use it), and is provided on an 'as is' basis. That means while it works for me, I can't guarantee that it'll work for you, or in every possible circumstance. Nor can I guarantee that it's completely error free.

 

Any feed back you have is welcome, while any questions about using it can be ask on this forum.

 

All the best,

 

Colin

 

[Malle Carrasco-Harris]

Colin,

Thank you for responding back in 12/12/15. Again, I'm working with copperhead spatial data and am currently trying to produce reliable and comparable KDEs using ArcGIS 10.3. However, variable choices are not (in my limited experience) frequently reported.
 

I had errors using the KDE tool and the PVC/Isopleth tool in the HRT toolbox and in the GME. It's probably something I am not doing correctly.
For KDE, I recieved these error messages when using the HRT:


"ERROR 999999: Error executing function.
The table name is invalid.
No spatial reference exists.
ERROR 010029: Unable to create the raster C:\GIS Work\SpatialDataAnalysis\CphdSptAnl.gdb\KDE_HRT_ 3413.
ERROR 010067: Error in executing grid expression.
Failed to execute (Kernel Density)."



I've been using ArcMET, however for the Density threshold Distances (SD's) and the Raster Expansion Ratio, I can't seem to find what the best values would be.

Do you have any experience choosing those numbers?

A SD of 1 vs the default 1000000 and a raster ratio of 1.1 vs 2.1 give different rasters in terms of how large the raster is and how "smooth" it appears (the bandwidth is set to h_ref). When I use the ArcMet PVC, it produces different PVCs depending on some of these factors listed above. Some PVCs are larger than others.

Any suggestions?

Best,

Malle 

[GIS in Ecology]

Hi Malle,

Sorry to take so long to respond to your post. By the looks of the error message you are getting, the problem is with the spatial reference for one of your data layers.The best thing to do is to go back and check the projection/coordinate system for your data frame, and for each of the data layers that you are using, and make sure that these are all the same, and that they are set to the one you want to use for your KDEs. You can do this in ArcGIS by bringing up the data frame properties and the data layer properties by right clicking on their names (one at a time) in the TABLE OF CONTENTS window and selecting PROPERTIES. If any of your data layers are not in the correct projection/coordinate system, then use the PROJECT tool to transform them into the projection/coordinate system that you want to use.

If you've double-checked all of this, and you are using the same projection/coordinate system for everything, and you're still getting this error message, then try repeating the KDE creation, but use a different folder to save the KDE in. Specifically, make sure that none of the folder names in the address have any spaces in the name (it looks like you have a space in the name of your folder C:/GIS Work, and this will cause problems with some tools - for GIS, it is best to get into the habit of always using an _ (underscore) rather than a space in file and folder names.

Finally, check that the point data layer you are using to generate your KDE has been loaded correctly by right clicking on its name in the TABLE OF CONTENTS window, and selecting OPEN ATTRIBUTE TABLE. If you have created this point data layer from a spreadsheet, .CSV or .TXT file, then you may need to specifically save it as a shapefile before you can use it to make your KDE layer (this is done by right-clicking on the point data layer's name in the TABLE OF CONTENTS window and selecting DATA> EXPORT DATA (I think this is the way round it is).

Once you've run through all these checks, if you're still having this problem, then post back on this thread, and I'll see what else I can suggest.

All the best,

Colin