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vegandevs / vegan

R package for community ecologists: popular ordination methods, ecological null models & diversity analysis
https://vegandevs.github.io/vegan/
GNU General Public License v2.0
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Adonis - how to calc the Sums of Squares using the Adonis output #439

Open MatS792 opened 3 years ago

MatS792 commented 3 years ago

Hi all, is there a way to get from the Adonis() function a matrix that contain the Sums of Squares or other values that are involved in the R squared calculation ? I am trying to compare the "variance explained" by two adonis calculated on the same matrix distance but with different grouping strategy. In other words: matrix.dist is calculated before running adonis. grouping_1 is the column within my_dataset with one type of grouping. grouping_2 is the column within my_dataset with an other type of grouping. The function I used: adonis1 <- adonis(matrx.dist ~ grouping_1, data = my_dataset, na.action = FALSE, perm = 9999) adonis2 <- adonis(matrx.dist ~ grouping_2, data = my_dataset, na.action = FALSE, perm = 9999)

Checking within adonis1 (for example), I found coef.sites which potentially could be the matrix that I'm looking for but I am not sure if coef.sites is the right one. Can you help me?

jarioksa commented 3 years ago

The adonis2 (the currently supported version) has column SumOfSqs in its output. This stands for "sums of squares". Did you ask about this? If you mean something else, please explain. [Checked in the current release 2.5-7 and the latest development version 2.6-0.]