Biodiverse version 4.1 released

[Shawn Laffan]

We are pleased to announce the release of Biodiverse version 4.1.

Versions for Windows, Mac and Linux (Ubuntu) are available and can be
accessed via https://github.com/shawnlaffan/biodiverse/wiki/Downloads


Installation instructions are at
https://github.com/shawnlaffan/biodiverse/wiki/Installation


Version 4.1 represents five issues closed across 96 source code commits.

Highlights of the changes since version 4.0 are at
https://github.com/shawnlaffan/biodiverse/wiki/ReleaseNotes#version-41,
and the related blog posts can be accessed via
https://biodiverse-analysis-software.blogspot.com/search/label/Version41

A more detailed listing of the closed issues is at
https://github.com/shawnlaffan/biodiverse/milestone/19?closed=1


The main user visible change is that z-score indices are now plotted
using a divergent colour scale using z-score significance thresholds. 
More details are in this blog post:
https://biodiverse-analysis-software.blogspot.com/2023/02/plotting-z-score-indices-and.html


If you have any questions about Biodiverse then please post a question
to this mailing list. You can also start a discussion at
https://github.com/shawnlaffan/biodiverse/discussions


Regards,
Shawn.

[Susana Gabriela Revollo Cadima]

Good afternoon,

I am working with this program, I really like how can I show which species in my phylogenetic tree are interacting in a specific point (cell). I want to know how can I download these trees?

Other question is in which environment could I open the scripts or work in, language in the scripts are not from RStudio. Or there is a form to work those scripts in RStudio?

Thank you

Susana Revollo Cadima  

[Shawn Laffan]

Hello Susana,

Trees can be downloaded from a range of locations.  Depending on what you are after you could try treebase, or perhaps extract data from the Open Tree of Life. 

The trees I work with a usually built by collaborators.

The Biodiverse code is written in Perl.  It is not too difficult to learn, and there are many resources available.  Just be sure to use recent resources as some of the older documents are out of date. 

If you prefer to use R for your scripts then we have an interface in development that will give access to the analysis engine (without the GUI) but it is not yet ready for release.  You can watch the development at https://github.com/shawnlaffan/BiodiverseR


Regards,
Shawn.

On 24/02/2023 13:56, Susana Gabriela Revollo Cadima wrote:

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[Susana Gabriela Revollo Cadima]

Thank you for your answer. I will try to use Perl.

I want to generate this kind of tree, for some specific areas 

[Shawn Laffan]

If you meant cluster dendrograms then they can be generated using the Cluster analyses. 


Can you provide more details of what you are trying to do? 

On 24/02/2023 15:40, Susana Gabriela Revollo Cadima wrote:

Some people who received this message don't often get email from suss...@gmail.com. Learn why this is important

Thank you for your answer. I will try to use Perl.

I want to generate this kind of tree, for some specific areas

To view this discussion on the web visit https://groups.google.com/d/msgid/biodiverse-users/37915463-2332-402c-b794-1fd1792a33a0n%40googlegroups.com.

[Susana Gabriela Revollo Cadima]

I already generated all the analysis. Then I want to export the trees that mark the presence of some clades in a particular area... for example when the cursor is over -17.25 and -68.30 I can see in the tree that 6 species are present in this area. There are a form to download this trees?

Sussy

[Shawn Laffan]

So what you want is the subtree for a cell? 

There is no tool that will give you a nexus file, for example, for an arbitrary cell.  There are ways of extracting subsets of data but they will not scale well if you have many species or many cells to process.  They could be added, though. 


If you want the set of branches in a cell then there are several indices that will give you those as lists, with the values being branch lengths, clade contributions, PE weights etc.  See for example the Labels on Tree index (https://github.com/shawnlaffan/biodiverse/wiki/Indices#labels-on-tree ) and the Phylogeneitc Endemism Lists index (https://github.com/shawnlaffan/biodiverse/wiki/Indices#phylogenetic-endemism-lists ).

The first index will add a list to each group (cell) called PHYLO_LABELS_ON_TREE.  When you export the data you can select this list to obtain a CSV file, for example.


Regards,
Shawn.

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