In ropensci/helminthR: Access London Natural History Museum Host-Helminth Record Database

helminthR

Programmatically access the London Natural History Museum's helminth database.

See software note in Ecography (available here)

Installation

From GitHub

# install.packages("devtools")
devtools::install_github("rOpenSci/helminthR")
library("helminthR")

From CRAN

install.packages("helminthR")

Main functions

`findHost()`

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)

`findParasite()`

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)

`data(locations)` and `findLocation()`

A data file containing all the location names that can be queried, along with putative latitude and longitude coordinates for the centroid of each location can be found in data(locations). Note that this will replace any object in the global environment named locations. 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)

Contribute!

Feel free to fork it and contribute some functionality.

Meta

Please report any issues or bugs.
License: GPL-3
Get citation information for helminthR in R doing citation(package = 'helminthR')
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.