Hi Manabu,
Yes, positivized is the same as taking the absolute value.
For some of Garland et al.'s diagnostic tests on contrasts you might
need the expected variances of the contrasts (actually, proportional
to their expected variance prior to standardization), or the
unstandardized
Ted Garland made the very good point to me that positivization is not
the same as taking the absolute value of contrasts when several traits are
being considered. If, for example, one is inclined to positivize the
contrasts for two traits with respect to trait x, then a pair of contrasts
Dear list,
I am trying to standardise independent contrasts following Garland et
al. (1992), but I am unsure just how you would extract the sum of it's
[contrast's] branch lenghts in R.
I computed independent contrasts using the pic function in ape. I
then took the contrasts and subtracted the
The contrasts returned by pic() should already be standardized.
Standardizing phylogenetic contrasts is performed by dividing each
contrast (calculated between internal or terminal nodes) by a sum
proportional to the square root of its expected variance. Assuming
Brownian motion, for two
