different results from vegan depending on input type #147
i am trying to use the adonis function in vegan to run the permanova analysis. but i am getting very different results depending on how i call adonis.
if i call adonis using a distance object such as the following:
bc=vegdist( data, method='bray')
i get a very different result than if i convert bc (a dist object) into a matrix:
bc=as.matrix( vegdist(data, method='bray') )
what is causing this difference and which is correct?
The text was updated successfully, but these errors were encountered:
You should supply either a distance object or data. If you supply a matrix, it is regarded as data and dissimilarities are calculated. So the following should be equivalent:
bc <- vegdist(data, method="bray") adonis(bc ~ var) adonis(data ~ var)
The second form you had would be equivalent to:
adonis(vegdist(as.matrix(vegdist(data))) ~ var)
which makes no sense. I suggest you follow the document and supply either a distance object or data.
Several functions accept either 'dist' object or raw data from which they calculate distances. If users supply their distances as square matrices (or data frames) these may be taken as raw data and we end up calculateing distances of distances. Most such functions had a test for symmetric square matrices that probably hold distances, but now these tests are made more consistent and robust. Should fix problems like issue #147