Some questions about phylogenetic diversity

[Wang]

Hello,Shawn

It's a pleasure to discuss this software with you, I'm having some difficulty using it to calculate phylogenetic diversity, I imported the genus, species, latitude and longitude data and imported the phylogenetic tree. The spatial index is established, and finally click Spatial to calculate PD. The following error occurred and I would like to know what caused it. During the entire calculation process, I performed the Remap element name operation on the phylogenetic tree, and an error was also reported.

[Shawn Laffan]

Hello Wang,

I think at least one of these issues was fixed in version 4. 

Can you try with the latest? 
https://github.com/shawnlaffan/biodiverse/wiki/Downloads


If that does not fix it then I will need to look at the code. 

Regards,
Shawn.

On 9/11/2023 12:26, Wang wrote:

You don't often get email from a2798...@gmail.com. Learn why this is important

Hello,Shawn

It's a pleasure to discuss this software with you, I'm having some difficulty using it to calculate phylogenetic diversity, I imported the genus, species, latitude and longitude data and imported the phylogenetic tree. The spatial index is established, and finally click Spatial to calculate PD. The following error occurred and I would like to know what caused it. During the entire calculation process, I performed the Remap element name operation on the phylogenetic tree, and an error was also reported.

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[Wang]

Hello,Shawn

I've used version 4.3 before, but it crashed recently. My firewalls are all turned off and I don't know what's causing this.

[Shawn Laffan]

Crashing is not good. 

The command window should stay open if this happens so you can copy the log text. 

Otherwise you can try to run it from the command line.  I can send instructions if you need them.

Shawn.

On 9/11/2023 13:31, Wang wrote:

You don't often get email from a2798...@gmail.com. Learn why this is important

Hello,Shawn

I've used version 4.3 before, but it crashed recently. My firewalls are all turned off and I don't know what's causing this.

在2023年11月9日星期四 UTC+8 09:47:19<Shawn Laffan> 写道：

Hello Wang,

I think at least one of these issues was fixed in version 4. 

Can you try with the latest? 
https://github.com/shawnlaffan/biodiverse/wiki/Downloads


If that does not fix it then I will need to look at the code. 

Regards,
Shawn.

On 9/11/2023 12:26, Wang wrote:

You don't often get email from a2798...@gmail.com. Learn why this is important

Hello,Shawn

It's a pleasure to discuss this software with you, I'm having some difficulty using it to calculate phylogenetic diversity, I imported the genus, species, latitude and longitude data and imported the phylogenetic tree. The spatial index is established, and finally click Spatial to calculate PD. The following error occurred and I would like to know what caused it. During the entire calculation process, I performed the Remap element name operation on the phylogenetic tree, and an error was also reported.

--
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To view this discussion on the web visit https://groups.google.com/d/msgid/biodiverse-users/1c9a5d90-af5c-49c2-8367-056532288af4n%40googlegroups.com.

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[Wang]

Hello,Shawn

My command window will be closed immediately when it pops up. I would like to trouble you to send me the command line operation method. I have another question to ask you. I don’t understand the meaning of the color stretch option. In addition, there is a bug as shown in the figure when importing map shape files. 

[Shawn Laffan]

I'll number the responses for clarity. 

1.
I think I know what is causing the crash.  It has been fixed in the development branch but I had thought it was due to code committed after 4.3 was released. 

I have uploaded a trial version with what should be the fix to the 4.3 release page at https://github.com/shawnlaffan/biodiverse/releases/tag/r4.3

Download and unzip the file called BiodiverseGUI_4.3a_test.exe.zip

Can you please try it? 


2.
To run Biodiverse from the command line you need to know where it is saved on your system.  Use the file explorer to find it, and then you can copy the address from the address bar.  Copy it into the command window and append the name of the Biodiverse executable. 

For example if you have saved it as BiodiverseGUI.exe is in a folder called C:\biodiverse then you might call it using:
C:\biodiverse\BiodiverseGUI.exe

3.
The colour stretches control how the values are plotted.  If you have a skewed distribution with a long tail then most of the colour range is applied to very few actual values.  Changing the colour stretch can help show some of the variations that are otherwise assigned the same colour.  This is a standard approach in GIS and remote sensing software (and others). 

4.
The shapefile error is not a bug.  The system is letting you know the shapefile does not overlap your data, probably because the coordinate systems differ. 

There are many general introductions to coordinate systems.  One is here https://www.crcsi.com.au/history-2/earth-observation-series-2/ (more specifically in Volume 2B, https://www.crcsi.com.au/assets/Earth-Observation/EO-Publication-Vol2B-UPDATED-72dpi.pdf ).

Regards,
Shawn.

To view this discussion on the web visit https://groups.google.com/d/msgid/biodiverse-users/0e469998-8332-4f1f-9017-3620432e7b13n%40googlegroups.com.

[Wang]

Thank you very much for your help, the problem has been solved

[Wang]

Hello,Shawn

I have another question for you. I imported the map outline. How can I color the empty areas outside the grid but within the outline?

在2023年11月9日星期四 UTC+8 15:50:15<Shawn Laffan> 写道：

[Shawn Laffan]

That's good to hear. 

I'll release official updates soon as this likely also affects Mac and Linux. 

Regards,
Shawn.

To view this discussion on the web visit https://groups.google.com/d/msgid/biodiverse-users/14ba8a1d-4e78-4964-b261-17261c48abcdn%40googlegroups.com.

-- 
Prof Shawn Laffan, FMSSANZ
  Director, Earth and Sustainability Science Research Centre
  School of Biological, Earth and Environmental Sciences
  UNSW, Sydney 2052, Australia
  Tel +61 2 9065 5607
  https://www.bees.unsw.edu.au/our-people/shawn-laffan
  https://www.unsw.edu.au/research/essrc
  https://shawnlaffan.github.io/biodiverse (free diversity analysis software)
  
  International Journal of Geographical Information Science
  http://www.tandf.co.uk/journals/ijgis

[Shawn Laffan]

At the moment this cannot be done. 

The visualisations in Biodiverse are relatively simple and are aimed at gaining an understanding of patterns rather than for cartographic purposes. 

I have opened an issue so it can be implemented at some point.  No promises for when, though. 
https://github.com/shawnlaffan/biodiverse/issues/891

More generally, creation of publication quality figures is best done using external software such as a GIS for spatial data and FigTree for trees.  There are also R libraries that can be used. 

Some relevant blogs posts are here:
https://biodiverse-analysis-software.blogspot.com/2019/05/reproduce-spatial-plots-with-same.html
https://biodiverse-analysis-software.blogspot.com/2018/08/cluster-analyses-export-coloured.html
https://biodiverse-analysis-software.blogspot.com/2017/04/biodiverse-now-exports-tree-branch.html


Regards,
Shawn.

On 10/11/2023 00:03, Wang wrote:

Hello,Shawn

I have another question for you. I imported the map outline. How can I color the empty areas outside the grid but within the outline?

To view this discussion on the web visit https://groups.google.com/d/msgid/biodiverse-users/a3a4d84d-573e-41f9-82d3-e9b342f5efcdn%40googlegroups.com.