[R] question about capscale (vegan)

[Gavin Simpson]

On Thu, 2006-11-16 at 17:25 +0100, Alicia Amadoz wrote:
> Hello,
> 
> I am interested in using the capscale function of vegan package of R. I
> already have a dissimilarity matrix and I am intended to use it as
> 'distance' argument. But then, I don't know what kind of data must be in
> 'comm' argument. I don't understand what type of data must be referred
> as 'species scores' and 'community data frame' since my data refer to
> nucleic distances between different sequences.

No, that is all wrong. Read ?capscale more closely! It says that you
need to use the formula to describe the model. "distance" is used to
tell capscale which distance coefficient to use if the LHS of the model
formula is a community matrix.

Argument "comm" is used to tell capscale where to find the species
matrix that will be used to determine species scores in the analysis,
*if* the LHS of the formula is a distance matrix. "comm" isn't used if
the LHS is a data frame, and "distance" is ignored if the LHS is a
distance matrix.

As you don't provide a reproducible example of your problem, I will use
the inbuilt example from ?capscale

## load some data
data(varespec)
data(varechem)

Now if you want to fit a capscale model using the raw species data, then
you would describe the model as so:

vare.cap <- capscale(varespec ~ N + P + K + Condition(Al), 
                     data = varechem,
                     distance = "bray")
vare.cap

In the above, LHS of formula is a data frame so capscale looks to
argument "distance" for the name of the coefficient to turn it into a
distance matrix. The terms on the RHS of the formula are variables
looked up in the object assigned to the "data" argument.

Now lets alter this to start with a dissimilarity/distance matrix
instead. The exact complement of the above would be:

dist.mat <- vegdist(varespec, method = "bray")
vare.cap2 <- capscale(dist.mat ~ N + P + K + Condition(Al), 
                     data = varechem,
                     comm = varespec)
vare.cap2

To explain the above example; first create the Bray Curtis distance
matrix (dist.mat). Then use this on the LHS of the formula. When
capscale now wants to calculate the species scores of the analysis it
will look to argument "comm" to use in the calculation; which in this
case we specify is the original species matrix varespec.

As for what are species scores, well this is a throw back to the origins
of the package and the methods included - all of this is related to
ecology and mainly vegetation analysis (hence vegan).

For species scores, read variable scores. The distance matrix (however
calculated) describes how similar your individual sites (read samples)
are to one another. You can also display information about the variables
used to determine those distances/similarities, and this is what is
meant by species scores. Whatever you used to generate the distance
matrix, the columns represent the info used to generate the "species
scores".

If some of this still isn't clear, email the list with the commands used
to generate your distance matrix in R and I'll have a go at explaining
this with reference to your data/example.

> 
> I would be very grateful if you could help me with this fact in any
> manner. Thank you in advance for your help.
> 
> Regards,
> Alicia

HTH

G

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