Code from: Costs of parasite generalism revealed by abundance patterns across mammalian hosts

Most parasites are able to infect several host species, yet generalism is anticipated to be a costly strategy. Parasite abundance provides an important indicator of fitness because it is promoted by longevity and fecundity, which are correlated with a parasite’s basic reproductive number. Using a global database of parasitic helminths of terrestrial mammals, we show that the abundance of parasitic helminths is phylogenetically structured across helminth species. High parasite abundance can be achieved through three separate components: infecting abundant host species, having a high infection success (prevalence), or achieving high parasite abundance within host individuals (infection intensity). Both phylogenetically specialist and generalist strategies can reach high abundances, but through different strategies. Specialist parasites achieve higher abundance than generalists on their principal host species but rely on host relatedness to infect multiple species. For generalist parasites, geographic overlap with, and diet similarity to principal host species are better predictors of parasite abundance. This study characterizes constraints on parasite host range and provides novel context to evaluate the potential for parasites to establish in new host species.

Methods
The underlying data is the Global Mammal Parasite Database, specifically v 2.0: http://dx.doi.org/10.1002/ecy.1799

It has been processed using a series of scripts in R (actually Rmd) which are archived in this repository