The following terms: D i, J i, σ ji, Φ i consist of (space) derivatives of primitive variables.
The partial own-resource elasticities, ε ii = ∂ lny i /∂ lns i, consist of only the direct effect, holding effort fixed.
The sets c i consist of vertices which are empirically observed to be related in the network, this could be for example, proteins identified in a mass-spectrometry proteomics pull-down, members of a cell signaling pathway, or co-authors of a publication.
The time for likelihood calculations on a partition i consist of a constant part (irrespective of the partition length), mainly the calculation of the P i matrix via exponentiation of the Q i matrix given the branch length t, that is, P i (t ) = e Q i t (Felsenstein, 2004).
For each compomer A i C j G k T l ∈ C x in a given collection of compomer spectra C ∑, we use I x (A i C j G k T l ) to denote the set of strings that (i) consist of i As, j Cs, k Gs, l Ts, (ii) contain exactly three distinct bases (i.e., three bases in the set Σ \ { x}), and (iii) are I-compatible with C ∑.
I know that all this is part of me, that it's what I consist of.
