Missing (or NA) data for PERMANOVA

[Anna1288]

I've searched around the threads on here and am not sure I am able to find what I'm looking for. I am hoping to use PERMANOVA to run my analysis, but I do have missing values. I don't seem to be able to run vegdist, adonis, or other related functions with blanks or NA. Is there any way around this?

[jarioksa]

It seems vegdist silently accepts NA values. It should not, and I'll see how to make it fail with NA unless requested.

The adonis and adonis2 functions do not accept NA values in vegan 2.5-x releases (I tagged this issue first as a bug because of this omission, but this is documented behaviour and hence no bug). The adonis function in the vegan development version 2.6-0 in GitHub handles NA with na.action argument. If you really need to handle NA values, you should use the GitHub version.

Alternatively, you can have listwise deletion of missing values using complete.cases function. Listwise deletion means that the observation is removed if any variable is missing. Here an example:

library(vegan)
data(dune, dune.env)
z <- dune.env
z[12,5] <- NA # one missing value
k <- complete.cases(z) # FALSE for rows with NA
adonis(dune[k,] ~ ., z[k,]) # use complete.cases as row selector

[jarioksa]

For the record: commit messages 2e9969a (and cherry-picked f4d5cae) suggest that na.rm was broken in vegan 2.4-2 (2016-09-07). Actually it was broken in 2.5-1 (2018-04-13) where we switched from .C() to .Call() interface: NA are always passed to the compiled code in .Call(), but optionally (like we did) in .C().