Reputation: 11
I'm currently performing an ANCOVA in R testing the difference in the levels of fungi depending on the types of fungi while correcting for a difference in the age of the fungi (days).
model <- aov(fungi_level ~ fungi_types + days, data = fungi_data)
Anova(model, type = "III")
Here, I find a significant difference between the different fungi types and want to perform post-hoc testing. As far as I can see there are (at least) two different ways to perform TukeyHSD:
TukeyHSD(model, which = 'fungi_types')
Which gives an error: "... non-factors ignored: days"
or
PostHoc <- glht(model, linfct = mcp(fungi_types = "Tukey"))
Does anyone know the difference between the two different tests? It seems that the glht is more restrictive when looking at the p-values.
Thanks a lot!
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