We propose a method for the non-parametric joint estimation of preferential attachment and transitivity in complex networks, as opposite to conventional methods that either estimate one mechanism in isolation or jointly estimate both assuming some functional forms. We apply our method to three scientific co-authorship networks between scholars in the complex network field, physicists in high-energy physics, and authors in the Strategic Management Journal. The non-parametric method revealed complex trends of preferential attachment and transitivity that would be unavailable under conventional parametric approaches. In all networks, having one common collaborator with another scientist increases at least five times the chance that one will collaborate with that scientist. Finally, by quantifying the contribution of each mechanism, we found that while transitivity dominates preferential attachment in the high-energy physics network, preferential attachment is the main driving force behind the evolutions of the remaining two networks.