[R-sig-eco] post-hoc test for adonis PERMANOVA

[Andre Rovai]

Dear friends,

I have been recently introduced to R and am dedicating myself to go deeper
on it. It can be tricky sometimes for a rookie, though!

I ran a PERMANOVA (vegan package) using the adonis() function and tried to
go deeper in the analysis by running a post-hoc test (betadisper()). I do
appreciate if someone more familiarized with codes related to the post-hoc
analysis could validate the way I am headed to. Here are the codes I used:

# permanova
fl.sem.transf.bray <- vegdist(fl, method="bray")
flfat <- read.table("flfator2.txt", header=T, row.names=1)
adonis(fl.sem.transf.bray ~ loc*trat, data=flfat, strata=flfat$trat,
permutations=999) # there was significant difference for the interaction

# post-hoc test
phoc <- with(flfat, betadisper(fl.sem.transf.bray, trat))
TukeyHSD(phoc)

Thank you!
Andre Rovai

[[alternative HTML version deleted]]

[asrovai]

Dear friends,

I have been recently introduced to R and am dedicating myself to go deeper
on it. It can be tricky sometimes for a rookie, though!

I ran a PERMANOVA (vegan package) using the adonis() function and tried to
go deeper in the analysis by running a post-hoc test (betadisper()). I do
appreciate if someone more familiarized with codes related to the post-hoc
analysis could validate the way I am headed to. Here are the codes I used:

# permanova
fl.sem.transf.bray <- vegdist(fl, method="bray")
flfat <- read.table("flfator2.txt", header=T, row.names=1)
adonis(fl.sem.transf.bray ~ loc*trat, data=flfat, strata=flfat$trat,
permutations=999) # there was significant difference for the interaction

# post-hoc test
phoc <- with(flfat, betadisper(fl.sem.transf.bray, trat))
TukeyHSD(phoc)

Thank you!
Andre Rovai




--
View this message in context: http://r-sig-ecology.471788.n2.nabble.com/post-hoc-test-for-adonis-PERMANOVA-tp7577678.html
Sent from the r-sig-ecology mailing list archive at Nabble.com.
[[alternative HTML version deleted]]

[Jari Oksanen]

There is a parametric post hoc test for betadisper(), but there is no post hoc test for adonis(). These two functions are different and study different null models. If anybody figures out how to do post hoc test for adonis() we may incorporate submitted code into vegan (though personally I think that the whole idea of post hoc tests is weird, to put it mildly).

Cheers, Jari Oksanen

Sent from my iPad

Post by Andre Rovai
Dear friends,
I have been recently introduced to R and am dedicating myself to go deeper
on it. It can be tricky sometimes for a rookie, though!
I ran a PERMANOVA (vegan package) using the adonis() function and tried to
go deeper in the analysis by running a post-hoc test (betadisper()). I do
appreciate if someone more familiarized with codes related to the post-hoc
# permanova
fl.sem.transf.bray <- vegdist(fl, method="bray")
flfat <- read.table("flfator2.txt", header=T, row.names=1)
adonis(fl.sem.transf.bray ~ loc*trat, data=flfat, strata=flfat$trat,
permutations=999) # there was significant difference for the interaction
# post-hoc test
phoc <- with(flfat, betadisper(fl.sem.transf.bray, trat))
TukeyHSD(phoc)
Thank you!
Andre Rovai
[[alternative HTML version deleted]]
_______________________________________________
R-sig-ecology mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

[asrovai]

Thank you Dr Oksanen!
Best,
André Rovai



--
View this message in context: http://r-sig-ecology.471788.n2.nabble.com/post-hoc-test-for-adonis-PERMANOVA-tp7577679p7577682.html
Sent from the r-sig-ecology mailing list archive at Nabble.com.