"Generates a matrix of taxa against replicates, with taxa on the y axis and replicate, sample, surveyEvent and survey on the x axis"
What I'm saying is because the matrix is focused on taxa, focus the wording around taxa, also note the requirement for four 'header' rows in the output: survey, survey event, sample and replicate.
I'd likely rename the description:
"Generates a matrix of taxa against replicates, with taxa on the y axis and replicate, sample, surveyEvent and survey on the x axis"
What I'm saying is because the matrix is focused on taxa, focus the wording around taxa, also note the requirement for four 'header' rows in the output: survey, survey event, sample and replicate.