[R] partial mantel tests "Ecodist"

[ddepew at sciborg.uwaterloo.ca]

Thanks Sarah,
Looking again at #2, I see your point.
As for the standardization, I didn't see it mentioned in the JSS  
paper, but I'll have another look.
Assuming a significant r is returned, I guess I would need to look at  
the raw data to infer the type of relationship (+ or -).


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David Depew
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Quoting Sarah Goslee <sarah.goslee at gmail.com>:

> Hi David,
>
> On Fri, May 8, 2009 at 10:27 AM,  <ddepew at sciborg.uwaterloo.ca> wrote:
>
>> My questions are as follows;
>>
>> 1) can "raw" data be used to construct the dissimilarity matricies? or
>> should they be standardized? different variables have different measurment
>> scales, my inclination is to standardize, but I don't know if this will
>> dampen relationships between variables.
>
> I'd standardize, especially if you're using Euclidean distances. The Goslee
> and Urban JSS paper on the ecodist package goes into more detail (as
> do some of the references cited therein).
>
>> 2) If env1 and another variable are correlated, is the appropriate test
>>        var1 ~ env1 + env2 + space?,
>> or
>>  var1 ~ env1 + space and then var1 ~ env2 + space?
>
> Test for what? The first one partials out both env2 and space from the
> relationship of var1 ~ env1, a very different thing than the second
> example.
>
>> 3) interpretation... Does the value of "r" (i.e. + or -) imply spatial
>> overlap (+) or spatial exclusion (-)?
>
> A negative value for r is usually uninformative (unless you've used
> particular data transformations or something otherwise unusual). The
> Mantel test question is generally: do differences in X correspond to
> differences in Y, so the test you want is whether r > 0. Again, see the
> JSS paper discusses this further.
>
> Sarah
>
> --
> Sarah Goslee
> http://www.functionaldiversity.org
>