Access to large host-parasite data is often hampered by the availability of data and difficulty in obtaining it in a programmatic way to encourage analyses. 'helminthR' provides a programmatic interface to the London Natural History Museum's host-parasite database, one of the largest host-parasite databases existing currently < http://www.nhm.ac.uk/research-curation/scientific-resources/taxonomy-systematics/host-parasites/>. The package allows the user to query by host species, parasite species, and geographic location.
See software note in Ecography (available here)
Given a host genus and (optionally) species and location, this function returns all host-parasite associations of a given host species. The example below determines all parasite records for helminth infections of Gorilla gorilla.
gorillaParasites <- findHost('Gorilla', 'gorilla')head(gorillaParasites)
Given a helminth parasite genus (and optionally species, and location), this function returns a list of host-parasite records for that parasite. In the example below, I query the database for occurrences of the genus Strongyloides.
strongHosts <- findParasite(genus='Strongyloides')str(strongHosts)
List all location names (
listLocations()). These names can be given to the
findLocation() function, which finds all host-parasite associations that have occurred in the given location. Below, I look at host-parasite associations recorded in France.
FrenchHostPars <- findLocation(location='France')str(FrenchHostPars)
Feel free to fork it and contribute some functionality.
helminthRin R doing
citation(package = 'helminthR')
Removed geocoding functionality previously present in listLocations(), as this now requires an API key. A cached version of the geographic coordinates of locations is provided as package data (
Added extra catch in
cleanDat.R to remove species who are identified as "something spp." instead of just removing those identified as "something sp.".