Update:
I think I tracked down the problem, but don't know how to fix it.
Using Condition() works fine with any of my other variables.

But, now I see that in this model
bees ~ FlowerType + condition(Transect)

While there are multiple observations on an given Transect, each transect has only one of numerous possible flower types.

And (I think this is the problem) some FlowerTypes only occur in one Transect. While other FlowerTypes are represented in multiple Transects. So for the FlowerTypes that only occur in one Transect, the repeated measures on those is the residual and must be messing up the analysis. Is that right?

If so, any suggestions on how to resolve the problem?

Thanks
Michael Wilson

------------------------------
-----------------------------
copied my first message below
-------------------------------


Hi, I'm having a problem with Capscale in Vegan.

When adding a Condition() statement in my formula, the Constraint in the formula seems to be ignored. I don't know if this is a problem with my formula, a bug, or if I don't understand something else.

Here is my R statement

bees.cap <- capscale(bees ~ FlowerType + Condition(Transect %in% FlowerType), envir, distance = "morisita", add=TRUE)

In my data, there are multiple observations at sites (Transect). Each site has one possible class factor (FlowerType). capscale works fine removing the Condition, and produces Scores for $Centroids. No Scores are produced for $Centroids when Condition is used. Strangely (to me anyway) the following three formulas give the same results.

bees ~ Condition(Transect)
bees ~ Transect + Condition(Transect %in% FlowerType)
bees ~ FlowerType + Condition(Transect)
bees ~ FlowerType + Condition(Transect:FlowerType)

The plot it produces the above produces is beautiful and agrees with what I observed in the field.

A plot without the Condition does agree with my sense of what I observed in the field, but the plot has a bad horeshoe, does not account for observations at the same Transect, and is harder to look at.

Does anyone have solutions/explanations?

Thank you so much.
Michael Wilson




	[[alternative HTML version deleted]]

