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)
listLocations()
and findLocation()
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)
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 doingcitation(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.