Dissimilarity matrices

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Josué Anderson R. Azevedo

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Dec 20, 2018, 8:02:33 AM12/20/18
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Dear Shawn Laffan,

Thanks for Biodiverse! It was a wonderful way of accessing biodiversity patterns!
 
I've been visually testing the results of the turnover metrics in Biodiverse, with especial interest in the RW_turnover. 
However, I've not been able to export pair-wise dissimilarity matrices. All I could get from the export menu were the values being displayed per cell like this:

ELEMENT,Axis_0,Axis_1,NEST_RESULTANT,RW_TURNOVER,RW_TURNOVER_A,RW_TURNOVER_B,RW_TURNOVER_C,SORENSON
-4250000:-2350000,-4250000,-2350000,0.300911854103343,0.931818181818182,6,8,74,0.872340425531915
-4450000:-1750000,-4450000,-1750000,0.617142857142857,0.863636363636364,12,2,74,0.76

How can I solve this?

Thanks!

Shawn Laffan

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Dec 21, 2018, 10:00:18 PM12/21/18
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Hello Josué,

I'm glad to hear you find it useful.  

It looks like you are running a spatial analysis in which you calculated a number of turnover indices.  These give you the rate of turnover between the set of labels groups (cells) in neighbor set 1, compared with the set of labels found in neighbour set 2.  These are turnover surfaces rather than matrices. 

To generate a pair-wise matrix of turnover values you need to run a cluster analysis, optionally skipping the step to run the cluster analysis itself.  You can then explore the results by clicking on individual cells to see the rate of turnover between that cell and each other cell in the data set.

The process is described in http://www.mssanz.org.au/modsim2011/E3/laffan.pdf , but without detailed steps. 

Rather than provide such steps here, I have added a blog post to describe the process.   
https://biodiverse-analysis-software.blogspot.com/2018/12/visualise-matrices-of-spatial-turnover.html

Note that the matrices can only be calculated for one index at a time, so if you want five indices then you will need to generate five matrices. 

Hopefully that helps, and please let me know if you need more details or have further questions.

Regards,
Shawn.
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Josué Anderson R. Azevedo

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Dec 27, 2018, 6:59:23 AM12/27/18
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Thank you for the explanation! I could now generate the pairwise matrices!
After spend sometime exploring the results, the only thing I still couldn't do was to visualize the turnover for each element as shown in the video. I got only the option of visualising the different clusters as shown in the screenshot.

I do have one more question (maybe for another topic?). Is it possible to run the analyses for a distribution of phylogenies using the GUI? I have managed to do it using the biodiverse pipeline in R for phylogenetic diversity, getting median values per grid cell for 100 different phylogenies. This would be very useful in the case of calculating RW Phylogentic turnover.

Thanks again!
Josué


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Josué Anderson R. Azevedo
University of Gothenburg, Sweden
Department of Biological and Environmental Sciences
Antonelli Research Group
ex_biodiverse.jpg

Shawn Laffan

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Dec 27, 2018, 10:10:03 PM12/27/18
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Hello Josué,

You can open the matrix from the outputs tab.  I need to update the blog post to show this.

WRT your other question, the GUI currently only runs one tree at a time.  I have scripts that can run multiple analyses, but not the matrices at this stage. 

Feel free to list it as an issue using the issue tracker - https://github.com/shawnlaffan/biodiverse/issues/

Regards,
Shawn.

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