longitudinal pairwise-differences : p-metric "shannon_entropy" instead of "shannon"


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

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

Yes, that is correct. Sample data was generated using earlier version of Qiime2 in which "shannon_entropy" was named "shannon".


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