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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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pairwise.adonis2 result is not consistent with the result of adonis2 #1609

Open holly2021FL opened 2 years ago

holly2021FL commented 2 years ago

Hi, Guys, recently I met with a question. the result of adonis2 shows p value is 0.18>0.05, however, the result of pairwise.adonis2 still shows some difference among several groups. Does anyone know the reason or how to solve this controversy? Here is the code adonis2(disc.wuf~sample_data(physeqD)$group, perm = 9999) metadata <- as(sample_data(physeqD), "data.frame") pairwise.adonis2(disc.wuf~group, data=metadata)**

holly2021FL commented 2 years ago

adonis2(disc.wuf~sample_data(physeqD)$group, perm = 9999) metadata <- as(sample_data(physeqD), "data.frame") pairwise.adonis2(disc.wuf~group, data=metadata)

cjfields commented 1 year ago

Hi @holly2021FL this is related to the adonis and adonis2 functions in the vegan package, not phyloseq. You should check the documentation and issues tracker there first, and if needed file a bug report there: https://github.com/vegandevs/vegan