class-weight parameter for rescript-evaluate evaluate-fit-classifier function

User Support
1

Hello,

Previously I had used the qiime feature-classifier fit-classifier-naive-bayes function as the last step to create my classifier. This function allowed me to use --i-class-weight as an option for input. However, I noticed that the newer qiime rescript-evaluate evaluate-fit-classifier function doesn't have this parameter. Is there another step that I'm missing with the rescript-evaluate plugin?

$ qiime --version
q2cli version 2026.4.0

$ qiime rescript-evaluate --version
QIIME 2 Plugin 'rescript-evaluate' version 2026.4.0 (from package 'rescript_evaluate' version 2026.4.0)
2

Hi @irvinng98,

The --i-class-weight parameter was not exposed in rescript-evaluate evaluate-fit-classifier. I've opened an issue here.

EDIT: See following comment.

3

Hi @irvinng98, after a quick discussion with @Nicholas_Bokulich, adding the option --i-class-weight to qiime rescript-evaluate evaluate-fit-classifier will likely lead to misleading results, as to properly test a weighted classifier requires a more sophisticated setup. Thus, it is recommended that the more appropriate evaluate-classifications via qiime rescript evaluate-classifications be run on your weighted / bespoke classifier.

4

Got it. Thank you so much for your help!