calculating R2 from anova.cca output (as a way to estimate effect size of terms)

[aguilart]

Hi! I have an anova..cca output from an rda object. I figure out that one could calculate effect sizes from these outputs as the proportion of the explain variance of each term relative to the total variance. However, now I have an rda object in which I had a Conditional and I am wondering whether the R2 I would calculate refer to the output of the conditional partialled out or not. Here an example:

rda_output <- rda(Y ~ X1*X2 + Conditional(Z), scale = T)

anov_cc_output <- as.data.frame(anova.cca(rda_output, by = "term", permutations = 9999)))

# estimating R2 as effect size

anov_cc_output$R2 <- anov_cc_outpu$Variance/sum(anov_cc_output$Variance)

So my, question is, that total variance I am calculating here (by summing the variance assigned to each term X1 and X2 and the residual), "includes" the variance explained by the Conditional or it is already partialled out?

Thanks!