no 'node_scale_root_height' (and other documentation issues)

[luka-sato]

In the readthedocs (code block [153]), there is a function called node_scale_root_height:

# scale tree to be 2X length of number of matrix cols
ctree = tree.mod.node_scale_root_height(spdata.shape[1] * 2)

However, I have tried running this bit of code, and got the following error: "AttributeError: 'TreeModAPI' object has no attribute 'node_scale_root_height'". The full documentation doesn't mention this, and when I click on "edge/dist changes" I get a 404 error.

[eaton-lab]

Hi Luka, Thanks for your patience, we are still working to update the documentation for the latest big updates. You can find this and other methods for modifying trees in the `mod` subpackage. The function you are looking for has been renamed `mod.edges_scale_to_root_height`. If you are using an interactive environment like jupyter or ipython you can use tab-completion to see all of the available options. [image: image.png] Best, Deren

…

On Tue, Nov 12, 2024 at 2:20 PM luka-sato ***@***.***> wrote: In the readthedocs <https://toytree.readthedocs.io/en/latest/Cookbook.html> (code block [153]), there is a function called node_scale_root_height: # scale tree to be 2X length of number of matrix cols ctree = tree.mod.node_scale_root_height(spdata.shape[1] * 2) However, I have tried running this bit of code, and got the following error: "AttributeError: 'TreeModAPI' object has no attribute 'node_scale_root_height'". The full documentation <https://eaton-lab.org/toytree/mod-topology/> doesn't mention this, and when I click on "edge/dist changes" I get a 404 error. Screenshot.2024-11-12.at.13.19.41.png (view on web) <https://github.com/user-attachments/assets/5995b37a-5cbc-4fd6-a70e-0c2f0d2e4c0a> — Reply to this email directly, view it on GitHub <#100>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGEVUG2A4KGELKE4WOJZMT32AJII5AVCNFSM6AAAAABRUZDJEWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGY2TGMBZGYZTMNA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Deren Eaton Associate Professor, Department of E3B Affiliate Member, Data Science Institute Committee on Equity and Diversity Columbia University https://eaton-lab.org <http://eaton-lab.org>

[luka-sato]

Thank you!