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permutest of dbrda fails with first=TRUE #198
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suggested fix to github issue #198: permutest (and hence anova) failed when first=TRUE was requested
I have fixes in branch issue-#198. I'll do some testing, and if successful, merge the issue branch to master. |
I assume I have fixed the bugs. There was some sloppy implementation that we didn't catch in testing when releasing the in RDA-style methods we define the fitted values of Y as Ŷ = HY, where H is the "hat matrix" or projection matrix derived from constraints (independent variables) X. In db-RDA we use Gower-transformed symmetric dissimilarity matrix G, and following Anderson, we find its fitted values as Ĝ = HGH, where H is exactly the same hat matrix as above. In Here a simple example to show the problem in old code and a verification it works after the fix. Both of the following would fail in mod <- dbrda(dune ~ A1 + Moisture, dune.env, dist="bray")
modc <- dbrda(dune ~ Condition(Management) + A1 + Moisture, dune.env, dist="bray") They will work after the fix. To see this, it is best to use a bit more controlled procedure: p <- shuffleSet(nrow(dune), 99) # create permutation matrix
p[1,] <- sort(p[1,]) # make first permutation identical to data
tst <- permutest(mod, first = TRUE, permutations = p)
tst$F.0 - tst$F.perm[1] # compare observed statistic to first permutation The observed statistic ( I'll merge this (with usual provision: nothing strange appears), and it will be included in the next release of vegan. |
Issue #198: permutest(<dbrda-result>, first = TRUE) fails
Solved and closed with PR #199 |
Cleo Tebby found the following code to fail:
It seems that the permutation results (
x$F.perm
) are given in complex format with zero imaginary component (e.g.,10.565131+0i
).The text was updated successfully, but these errors were encountered: