Dear R-users I applied vegan's varpart function to partition the effects of explanatory matrices. Adj. R square for the unique fraction [a] is 0.25. Does anyone know why the decomposition by hand using rda gives me a different result for [a] (constrained proportion is 0.32)? I used cbind() for the conditional fractions, but it should be similar to condition()?
Thanks very much Sibylle > AZ_var<-varpart(AZ, OeAF, Acker, Gruen) > plot(AZ_var) > > AZ_var Partition of variation in RDA Call: varpart(Y = AZ, X = OeAF, Acker, Gruen) Explanatory tables: X1: OeAF X2: Acker X3: Gruen No. of explanatory tables: 3 Total variation (SS): 239101 Variance: 1811.4 No. of observations: 133 Partition table: Df R.square Adj.R.square Testable [a+d+f+g] = X1 29 0.55103 0.42463 TRUE [b+d+e+g] = X2 11 0.12135 0.04147 TRUE [c+e+f+g] = X3 9 0.23870 0.18300 TRUE [a+b+d+e+f+g] = X1+X2 40 0.64676 0.49318 TRUE [a+c+d+e+f+g] = X1+X3 38 0.59086 0.42546 TRUE [b+c+d+e+f+g] = X2+X3 20 0.36936 0.25675 TRUE [a+b+c+d+e+f+g] = All 49 0.69072 0.50813 TRUE Individual fractions [a] = X1 | X2+X3 29 0.25139 TRUE [b] = X2 | X1+X3 11 0.08268 TRUE [c] = X3 | X1+X2 9 0.01495 TRUE [d] 0 -0.00893 FALSE [e] 0 -0.01412 FALSE [f] 0 0.20033 FALSE [g] 0 -0.01816 FALSE [h] = Residuals 0.49187 FALSE Controlling 1 table X [a+d] = X1 | X3 29 0.24246 TRUE [a+f] = X1 | X2 29 0.45171 TRUE [b+d] = X2 | X3 11 0.07375 TRUE [b+e] = X2 | X1 11 0.06856 TRUE [c+e] = X3 | X1 9 0.00083 TRUE [c+f] = X3 | X2 9 0.21528 TRUE --- Use function 'rda' to test significance of fractions of interest > rda(AZ, OeAF, cbind(Acker, Gruen)) Call: rda(X = AZ, Y = OeAF, Z = cbind(Acker, Gruen)) Inertia Proportion Rank Total 1811.3728 1.0000 Conditional 669.0542 0.3694 20 Constrained 582.0993 0.3214 4 Unconstrained 560.2193 0.3093 4 Inertia is variance Eigenvalues for constrained axes: RDA1 RDA2 RDA3 RDA4 570.343 8.310 1.833 1.614 Eigenvalues for unconstrained axes: PC1 PC2 PC3 PC4 533.129 12.619 11.618 2.854 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.