dkahle / dkahle/TITAN2

100% occurrence detected 1 times

Open
#9 2 comments 0 reactions 0 assignees View on GitHub
Dominant language
HTML
Stars
16
Forks
4
PR merge metrics
No merged PRs in 30d

Description

Hello -
I am trying to use the TITAN function and am following the vignette. I continue to get the following error. I am using 16s rRNA data and have ASVs as my taxa matrix. I have transformed to relative abundance and tried to remove taxa that are not present in 5 or more samples. I have tried filtering a few ways and still keep getting this same error.

100% occurrence detected 1 times (100.0% of taxa),
use of TITAN less than ideal for this data type.
taxa frequency screen complete.
Partitioning along gradient...
Error in env.part(env, taxa, minSplt = minSplt, messaging = messaging) :
Number of sites not equal between env vector and taxa matrix

I am not sure why I am getting that my number of sites is not equal between the env vector and taxa matrix. Both of my data frames have 69 rows made up of the "sources". The taxa matrix has bacterial ASVs as columns.

Can you give more details on both parts of this error (100% occurrence and number of sites).

Thank you,
Mia

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with the TITAN function and the env.part error shown in the report. Reproduce the call using the described 69-row environmental vector and taxa matrix, then inspect how the occurrence screen and site-count check are reached. Done means explaining or correcting the reported occurrence warning and the mismatch error, with a focused regression test if a reproducible case can be obtained.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.