Hello,
Thank you for providing this valuable tool.
I encountered an issue while working with my data generated by the following command:
qiime diversity alpha --i-table table.qza --p-metric shannon --o-alpha-diversity shannon.qza
I had trouble with the longitudinal pairwise-differences command in
https://docs.qiime2.org/2023.9/tutorials/longitudinal/#pairwise-difference-comparisons
qiime longitudinal pairwise-differences
--m-metadata-file ecam-sample-metadata.tsv
--m-metadata-file shannon.qza
--p-metric shannon
--p-group-column delivery
--p-state-column month
--p-state-1 0
--p-state-2 12
--p-individual-id-column studyid
--p-replicate-handling random
--o-visualization pairwise-differences.qzv
I received the following message:
Plugin error from longitudinal:
metric must be a valid metadata or feature table column
I don't have this error with the sample data provided in the documentation.
To resolve this issue, I specified --p-metric shannon_entropy instead of shannon in the qiime longitudinal pairwise-differences command. I would like to confirm if this is an appropriate solution.
Thank you for your assistance, and have a great day!
Jérémy Tournayre