Accesses parasite occurrence records from the London Natural History Museum's Host-Parasite database, which contains over a quarter of a million helminth records.
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README.md

helminthR

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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 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.

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