I always have some problems with the formula while doing PERMANOVA. For example, adonis(distance.bray ~ x+y, sample.data, permutations = 999) and adonis(distance.bray ~ y+x, sample.data, permutations = 999) gave me the different results of the R square values for factor x and y. So what are the difference between these two formula? And which one should I trust?
Also, I once did the analysis with three factors. When I did adonis(distance.bray ~ x+y+z, sample.data, permutations = 999), z was significant. But when I do adonis(distance.bray ~ z, sample.data, permutations = 999), z was not significant. Can someone explain what happened in these analyses?
Hi,
Please take a look at this question and the answer: https://stats.stackexchange.com/questions/312302/adonis-in-vegan-order-of-variables-non-nested-with-one-degree-of-freedom-for
In short, the output of `adonis` says: "Terms added sequentially (first to last)". That means that the order matters. And from the answer:
> This occurs because A1 and Moisture are not uncorrelated; as there is some linear dependency, which ones goes into the model first determines how much variation is left to be explained by the second of the pair of covariates.
Please, take a look at the link. Here you can find what you can do in such cases.
Hi,
Please take a look at this question and the answer: https://stats.stackexchange.com/questions/312302/adonis-in-vegan-order-of-variables-non-nested-with-one-degree-of-freedom-for
In short, the output of `adonis` says: "Terms added sequentially (first to last)". That means that the order matters. And from the answer:
> This occurs because A1 and Moisture are not uncorrelated; as there is some linear dependency, which ones goes into the model first determines how much variation is left to be explained by the second of the pair of covariates.
Please, take a look at the link. Here you can find what you can do in such cases.
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