vegandevs/vegan — pull request #41 by jarioksa (2014-09-16 17:53:07+00:00)
Title: Delete ccanova* in favour of anova.cca*

When `anova.cca*` switched to parallel processing, the old code was backed up as `ccanova* ` functions. This PR suggests that these functions re removed and only the new `anova.cca*` functions remain.

The new `anova.cca*` functions are basically similar, but with a new interface (as they use **permute** API). The most important change is that adaptive selection of the number of permutations was dropped in new `anova.cca()`.

The new `anova.cca` do **not** pass all `tests/vegan-tests.R`: models with missing values cannot always be handled in all cases. I don't think there is anything fundamental, but using the same permutation matrix with missing data brings along problems. These issues are commented in commit 1f2467fc