PD based on branch length back to the last shared ancestor

[Editor PDCA]

Hi Shawn, 

I would be very obliged for your help with the analysis of phylogenetic diversity. In my analysis I have no problems with PD based on branch length back to the root of the tree, but when I try PD based on branch length back to the last shared ancestor, I get the following message:

Can't use an undefined value as an ARRAY reference at C:\Users\ADMIN\AppData\Local\Temp\par-41444d494e\cache-

5d92c0342f8b0485a4f97287558a340043bcf5f1\inc\lib/Biodiverse/Spatial.pm line

1023.

Where is the problem?

Many thanks in advance.

Sergei

[Shawn Laffan]

Hello Sergei,

Which version of Biodiverse are you using? 

I cannot reproduce it using my own test files.  It is possible this is an issue that has been fixed in a more recent version. 

If you are using the latest version then is there some way you can share the files with me?  (If you are willing to do so). 

Regards,
Shawn.

On 11/07/2023 17:31, Editor PDCA wrote:

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[Shawn Laffan]

The issue occurs when the analysis works on a group that has no labels on the tree. 

I have a fix that will be in the next version of Biodiverse ( https://github.com/shawnlaffan/biodiverse/issues/873 ).

Until that is released the basedata can be trimmed to match the tree so that the condition does not occur.  Note that labels not on the tree are ignored in the PD calculations so this will not affect any of the resulting values. 

Thanks to Sergei for providing test data.

Shawn.

To view this discussion on the web visit https://groups.google.com/d/msgid/biodiverse-users/b38158bf-91d7-5110-a693-579099617500%40unsw.edu.au.