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On Jan 6, 2021, at 5:32 PM, Shawn Laffan <shawn....@unsw.edu.au> wrote:
Hello Becks,
Those data can be imported using matrix format. You will need to delete the current first line so the header comes first.
It would also be helpful to change the file name extension to txt so the file selection system shows it by default. Otherwise you need to change the "txt and csv files" widget at the bottom right to "all files". This is not essential, but does save some button clicking.
On the screen after the file selection, set the "data are in matrix form?" checkbox to on.
As your data are in a sites-as-columns format, they need to be imported in transposed form (OTUs as groups, caves as labels). When selecting the columns, set the OTU as text_group and the site columns as labels (see first screen shot below).
Once the data are imported, choose the Basedata > Transpose menu option to create a basedata with the caves as the groups and the OTUs as the labels (second screenshot shows what this will look like).
In regards to linking the basedata and the tree, Biodiverse knows nothing about the Linnean system of taxonomy - all it sees is text and numbers. This is why we refer to labels. (A similar principle applies to groups). So long as the labels in the basedata match the terminal names on the tree then the analyses will work. There is a remap system for cases where they do not match: https://biodiverse-analysis-software.blogspot.com/2017/04/matching-spatial-tree-matrix-and.html
WRT the abundance data, keep them. They have no effect on endemism analyses, and might become useful later if you want to run some of the abundance weighted indices.
Once you have it all imported then you can run the various indices, followed by randomisations as needed. Some of the RPD/RPE indices might also be useful. These use the topology of the tree which can be useful for a variety of reasons (see for example Mishler et al. 2014, 2020).
https://doi.org/10.1038/ncomms5473
https://doi.org/10.1111/jse.12590
I am not aware of direct use of microbial data with Biodiverse, but as I noted above it is all numbers. More generally, Phylogenetic Diversity (PD) has been used for such data in the past (as a start look for UniFrac, and also https://doi.org/10.1371/journal.pcbi.1002832 ). You can run whatever analyses you like with whatever data you like - the important differences are usually in how the data are interpreted (the first step checking they make sense, of course).
For further reading about Biodiverse, have a look at the blog and also the publications list.
https://biodiverse-analysis-software.blogspot.com/ (for posts on the randomisations, see https://biodiverse-analysis-software.blogspot.com/search/label/randomisations ).
https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList
Please do ask if you have any further questions. Success stories are also always welcome.
Regards,
Shawn.
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Aloha Shawn,
Thanks very much for the details below. I have run into a problem - I am using a Mac (OS Catalina 10.15.5). So far, I have not been able to get Biodiverse to be able to access the files. I did try going into security and giving access via “full access", but did not work. See the screen shot below. Do you have any recommendations to get Biodiverse access? If I have missed this somewhere in the documentation, my apologies!
CheersBecks
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-- Prof Shawn Laffan, FMSSANZ School of Biological, Earth and Environmental Sciences UNSW, Sydney 2052, Australia Tel +61 2 9385 8093 https://www.bees.unsw.edu.au/our-people/shawn-laffan https://shawnlaffan.github.io/biodiverse (free diversity analysis software) International Journal of Geographical Information Science http://www.tandf.co.uk/journals/ijgis UNSW CRICOS Provider Code 00098G
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/home/username/biodiverse
is one workaround.
The error does not occur when calling the script directly from a command terminal instead of the Finder:
/Applications/Biodiverse.app/Contents/MacOS/Biodiverse
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