[R] Vegan(ordistep) error: Error in if (aod[1, 5] <= Pin) { : missing value where TRUE/FALSE needed

[Jari Oksanen]

Nevil Amos <nevil.amos <at> monash.edu> writes:

> 
> I am getting the following erro rmessage in ordistep.  I have a number of
> similarly structured datasets using ordistep in a loop, and the message
> only occurs for some of the datasets.
> 
> I cannot include a reproducible sample  - the specific datasets where this
> is occur ing are fairly large and there are several pcnm's in the rhs of
> the formula.
>
> Error in if (aod[1, 5] <= Pin) { : missing value where TRUE/FALSE needed
>
Nevil,

It seems to me that the source of the problem appears in this table:

>              Inertia Proportion Rank
> Total          1.8110     1.0000
> Conditional    0.8681     0.4793   32
> Constrained    0.0000     0.0000    0
> Unconstrained  0.9429     0.5207   29
> Inertia is variance
> Some constraints were aliased because they were collinear (redundant)
> 

The key point is that "Constrained" component is completely alaised (Inertia 0,
Rank 0) and therefore it cannot be analysed in permutation tests. You get the
same error message with this model:

mod <- rda(dune ~  Moisture + Condition(Moisture), dune.env)

and for the same reason. In your case, PCNM's seem to explain everything and
there is nothing left for other variables, and therefore you cannot analyse them.

Cheers, Jari Oksanen

I can see how to fix this in vegan. All I can do is to handle these cases
smoothly and with comprehensible error messages, though. They cannot be handled
with permutation tests since there is nothing to do if "Constrained" component
is zeroed.

Cheers, Jari Oksanen