Working with continuous data

[weevil-see]

Hi,
thank you for creating the script, it's super helpful!

I needed to analyze continuous characters, which need to be standardized so that they contribute to the results in the same proportions (https://www.researchgate.net/publication/323615953_A_guide_for_the_analysis_of_continuous_and_landmark_characters_in_TNT_Tree_Analysis_using_New_Technologies).

So I added the line:

nstates stand [highest value amonst continued caracters] [list of continuous characters to be standardized, separated by space only];

after those lines:

/*Reopen tnt*/
if ('istnt' || 'isnex')
  procedure $input;

In my case, the highest value is 2.8 and I have 3 continuous characters, so the line reads as: nstates stand 2.8 0 1 2;

Just thought this might be helpful to anyone who is facing the same problem!

Best,
Jakob

[starsareintherose]

Hello, would you mind use Pull Request to contribute that, therefore your contribution will be seen by others

[weevil-see]

The problem is: The nstates stand command needs the highest value amongst continued characters, and the list of continuous characters to be standardized. Those values would need to be defined by the script itself, or they would need to be passed as an additional option when running the tnt run guoyi.run filename command. I don't know how to implement this, that's why i modify the values directly in the guoyi.run file.

Edit: I just opened a pull request for the readme instead

[starsareintherose]

I will think about that. Actually this script can process continuous characters, the only character it can't process is landmark now, I will handle them in the future.

[weevil-see]

But it's not standardizing the characters, right? At least my trees are more resolved when I add the nstates stand line.

[starsareintherose]

Could you tell me how commonly data standardization is applied prior to phylogenetic tree inference? Are there any published studies that have used this approach?

If so I may need to consider re-frame current script