a reply to Haegeman and Loreau

Haegeman and Loreau published a paper that is primarily a criticism of a maximum entropy model of trait-based community assembly (by Shipley et al.) and purports to show the limitations of this method in ecology. However, they misunderstood the basic purpose, logic and justification of the maximum entropy formalism and, because of this, leveled criticisms of Shipley et al. that are unfounded. Part of the confusion can be traced to sloppy presentation of the underlying approach in Shipley et al. The confusion arises because maximum entropy models are justified based on information theory and Bayesian logic while the interpretation that Haegeman and Loreau present is based on substantive empirical assumptions about microstate allocations and a combinatorial argument that do not apply to maximum entropy models and which I do not apply to my model in particular. The maximum entropy formalism was developed in its modern form by Jaynes (1957a, 1957b, 1971, 1983a, 1983b) and is described most completely in his posthu-mously published book (Jaynes 2003). My colleagues and I (Shipley, Vile and Garnier 2006) (hereafter SVG) used this formalism to translate the notion of community assembly through trait-based environmental filtering into mathema