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So help would be much appreciated!

I have already completed a CCA plot which shows 7 sites, about 15 species and 6 environmental variables. However, it is saying that the unconstrained axis is 0 and I cannot complete an ANOVA on my CCA results in order to see what the significance of the axes are. I also attempted to use the spenvcor function to see the environmental to species correlation and it is giving me 1's for all of the axes.

So I am definitely doing something wrong but I just can't figure out what. Here is my code:

MayEnviro <- read.csv("MayEnviro.csv", header=TRUE)
MaySpecies <- read.csv("MaySpecies.csv", header=TRUE)
t <- cca(MaySpecies,
         MayEnviro[, c("AFDM","Chla","Chloride","TSS","TN","TP","Velocity")])
spenvcor(t)
Gavin Simpson
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user3434003
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1 Answers1

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The number of axes you can derive from a data set with n = 7 sites, m = 15 species is min(n, m) - 1, which is 6. As you also have 6 constraints (the environmental variables) you explain the data exactly and there is no residual variance to work with. In fact there are no constraints on the solution and the result is just like CA.

In this instance, with so few sites, you should look to fit a model with fewer constraints, say 2 or 3 at most.

Gavin Simpson
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