[R] varpart

[Jari Oksanen]

Sibylle Stöckli <sibylle.stoeckli <at> gmx.ch> writes:

>
> 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()?
...
                        Df R.square Adj.R.square Testable
...
> [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
...

Sibylle,

When you decompose by hand, you probably calculate

X1 | X2+X3 = All - X2+X3, or

0.32136 = 0.69072 - 0.36936,

whereas varpart function in vegan calculates this as

0.25139 = 0.50813 - 0.49318 (with smaller round-off error).

That is, vegan uses column "Adj.R.square", but you used column "R.square"
in your hand calculation.

This is documented in ?varpart with a reference to publications where
this is justified (Peres-Neto et al. 2006, Legendre & Legendre 2012).

Sorry for excessive pruning of your original post: I use gmane to 
post and it does not allow appropriate quoting of the original 
message.

Cheers, Jari Oksanen