R help - May 2009 - partial mantel tests "Ecodist"

Hi all,
I'm searching for a little clarification on partial mantel tests  
(ecodist package)

I've a distance matrix (x,y), and several others containing  
environmental/chemical variables.
Based on the help file, and the package instructions I've managed to  
implement the tests as;

var1 ~ env1 + space

to partial out the effect of space and test the relationship between  
the variable of interest vs variable env1.

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.

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?

3) interpretation... Does the value of "r" (i.e. + or -) imply spatial
overlap (+) or spatial exclusion (-)?

Any assistance would be greatly appreciated!

Thanks,


-- 
David Depew
PhD Candidate
Department of Biology
University of Waterloo
200 University Ave W
Waterloo, Ontario, Canada
N2L 3G1

T:(1)-519-888-4567 x 33895
F:(1)-519-746-0614

ddepew at scimail.uwaterloo.ca
http://www.science.uwaterloo.ca/~ddepew

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

Dear all,

I am trying to calculate barriers with the monmonier algorithm
(adegenet).

mon1 <- monmonier(mycoordinates, mydistancamatrix, network$cn, ...)

The network beforehand looked alright. However, I always get the error:
"cn is not a nb object". I am not really sure what this means,
probably
that the network is not recognised properly. So far I was not able to
detect my fault, though I already installed the newest version of R and
updated all packages (which was suggested in help files I have found
during the search). Any help would be highly appreciated!

Thanks in advance!

Best regards
Johannes