In getPrevalence (code) documentation, the difference between detection and prevalence is not very clear.
Prevalence is a common term in biology, but detection is much less. It's nicely explained in OMA:
The function arguments detection and as_relative can also be used to access how many samples pass a threshold for raw counts. Here, the population prevalence (frequency) at the absolute abundance threshold (as_relative = FALSE) at read count 1 (detection = 1) is accessed.
Can be rewritten
Detection threshold for absence/presence. If as_relative = FALSE, it sets the counts threshold for a taxon to be considered present. If as_relative = TRUE, it sets the relative abundance threshold for a taxon to be considered present.
Or we can rewrite the Details section to clarify this aspect with a couple of examples.
antagomir
commented
3 weeks ago
In
getPrevalence(code) documentation, the difference betweendetectionandprevalenceis not very clear.Prevalence is a common term in biology, but
detectionis much less. It's nicely explained in OMA:Can be rewritten
Or we can rewrite the
Detailssection to clarify this aspect with a couple of examples.