Given a simple undirected graph $G$ there is a simplicial complex $\mathrm{Ind}(G)$, called the independence complex, whose faces correspond to the independent sets of $G$. This is a well studied concept because it provides a fertile ground for interactions between commutative algebra, graph theory and algebraic topology. One of the line of research pursued by many authors is to determine the graph classes for which the associated independence complex is Cohen-Macaulay. For example, it is known that when $G$ is a chordal graph the complex $\mathrm{Ind}(G)$ is in fact vertex decomposable, the strongest condition in the Cohen-Macaulay ladder. In this article we consider a generalization of independence complex. Given $r\geq 1$, a subset of the vertex set is called $r$-independent if the connected components of the induced subgraph have cardinality at most $r$. The collection of all $r$-independent subsets of $G$ form a simplicial complex called the $r$-independence complex and is denoted by $\mathrm{Ind}_r(G)$. It is known that when $G$ is a chordal graph the complex $\mathrm{Ind}_r(G)$ has the homotopy type of a wedge of spheres. Hence it is natural to ask which of these complexes are shellable or even vertex decomposable. We prove, using Woodroofe's chordal hypergraph notion, that these complexes are always shellable when the underlying chordal graph is a tree. Further, using the notion of vertex splittable ideals we show that for caterpillar graphs the associated $r$-independence complex is vertex decomposable for all values of $r$. We also construct chordal graphs on $2r+2$ vertices such that their $r$-independence complexes are not sequentially Cohen-Macaulay for any $r \ge 2$.