betadisper with NAs not passing R CMD check under R Devel

[gavinsimpson]

Kurt Hornik reports that under R Devel on CRAN that betadisper() is throwing an error on the examples in ?betadisper, in particular when the groups and distances have NAs:

> mod2 <- betadisper(dis, groups) ## warnings
Warning in betadisper(dis, groups) :
  missing observations due to 'd' removed
Error in optim(apply(X, 2, median, na.rm = TRUE), fn = medfun, gr = dmedfun, :
  non-finite value supplied by optim
Calls: betadisper -> spatialMed -> ordimedian -> optim

There is clearly something wrong as the code doesn't even recognise that there are missing values in group yet there are.

[gavinsimpson]

This is now fixed in devel version of vegan. I just need to cherry pick the set of commits into the current CRAN branch.

[jarioksa]

There are droplevels in centroids.cca, envfit.default and factorfit. Are they infected?

I think that most of changes could be merged to 2.4-1. I'll have a look at merges next week.

[gavinsimpson]

If droplevels is used on factor with NAs, these will get removed unless we set exclude = NA in the call to droplevels. I haven't looked at those other functions yet but unless we're doing something subsequent testing for missingness in factors whose levels have been dropped, we should be OK. If we want to preserve behaviour prior to this recent change we should probably add exclude = NA as before this change droplevels was defined as factor(x, ...) and hence we got factor(x, ..., exclude = NA) as that is the default. Now we will get factor(x, ..., exclude = NULL) which works weirdly if the factor contains NA.

To be safe we probably should be explicit about excluding NA... so droplevels is truly no-op.

[jarioksa]

Got to check these functions plus other functions which use factor() or as.factor(). They are many (anosim, clamtest, dispweight, factorfit, hierParseFormula, kendall, meandist (explicit factor(grouping, exclude = NULL)), mrpp, permatfull, permatswap, and some plot functions).