Abstract
In this paper, we expand on the notion of combinatorial presheaf, first introduced explicitly by Aguiar and Mahajan in 2010 but already present in the literature in some other points of view. We do this by adapting the algebraic framework of species to the study of substructures in combinatorics. Afterwards, we consider functions that count the number of patterns of objects and endow the linear span of these functions with a product and a coproduct. In this way, any well-behaved family of combinatorial objects that admits a notion of substructure generates a Hopf algebra, and this association is functorial. For example, the Hopf algebra on permutations studied by Vargas in 2014 and the Hopf algebra on symmetric functions are particular cases of this construction. A specific family of pattern Hopf algebras of interest are the ones arising from commutative combinatorial presheaves. This includes the presheaves on graphs, posets and generalized permutahedra. Here, we show that all the pattern Hopf algebras corresponding to commutative presheaves are free. We also study a remarkable non-commutative presheaf structure on marked permutations, i.e. permutations with a marked element. These objects have a natural product called inflation, which is an operation motivated by factorization theorems for permutations. In this paper, we find new factorization theorems for marked permutations. We use these theorems to show that the pattern Hopf algebra for marked permutations is also free, using Lyndon words techniques.