metacom performs the Elements of Metacommunity Structure analysis. This analysis aims to classify metacommunites based on the combination of three statistics (coherence, turnover, and boundary clumping). The analysis is performed on site-by-species matrices depicting the distribution of species among sites, but can also be used to examine any similarly bipartite interaction (plant-pollinator, host-parasite, etc.).
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helminthR allows for the programmatic access of London Natural History Museum’s helminth database. This extensive database is composed of over 250,000 host-parasite occurrence records from all over the globe.
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insectDisease is a data package which documents and serves the Ecological Database of the World’s Insect Pathogens. This is a database of known pathogens of many species of insects and other arthropods. This database was designed by David Onstad, and first described in Braxton et al (2003). The database is somewhat unique in that in addition to host-parasite associations that occur in nature, it also contains some true host absences: records of instances where a given host species was inoculated with a pathogen and found not to be susceptible to it. This database also contains a large amount of ecological data on hosts and parasites. Here, we document and preserve these data as an R package, also providing csv flatfiles in the csv folder and an interactive web platform.
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Hmsc contains functions to fit a joint species distribution model (JSDM), analyze the output, and to generate predictions with these trained models. The required data for a HMSC analysis includes a matrix of species occurrences or abundances and a matrix of environmental covariates. Optionally, the user can include information species traits, phylogenetic relationships and information on the spatiotemporal context of the sampling design to account for dependencies among the sampling units.
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