I am using protest (in vegan) to assess the concordance between NMDS
scores, as shown below:
fishbug.fit <- protest(scores.bug, scores.fish,permutations = 9999)
I would like to get the average residuals from protest. When I use
residuals(),
resids.fit<-residuals(fishbug.fit)
which residuals is this returning to me? Are these the average
residuals from the 9999 permutations or are these the residuals from the
most recent permutation?
Thanks for any help,
--Chris
residual with protest in vegan
2 messages · Christopher Chizinski, Tyler Smith
Christopher Chizinski <chizi001 at umn.edu> writes:
I am using protest (in vegan) to assess the concordance between NMDS scores, as shown below: fishbug.fit <- protest(scores.bug, scores.fish,permutations = 9999) I would like to get the average residuals from protest. When I use residuals(), resids.fit<-residuals(fishbug.fit) which residuals is this returning to me? Are these the average residuals from the 9999 permutations or are these the residuals from the most recent permutation?
The residuals are from the unpermuted procrustes test. Compare: residuals(protest(scores.bug, scores.fish)) residuals(procrustes(scores.bug, scores.fish, symmetric = TRUE)) Cheers, Tyler --