Access London Natural History Museum Host-Helminth Record Database

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.


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See software note in Ecography (available here)

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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News

helminthR 1.0.7

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 (data(locations)).

Added extra catch in cleanDat.R to remove species who are identified as "something spp." instead of just removing those identified as "something sp.".

helminthR 1.0.6

  • bug fix that was causing null results for some location specifications.

helminthR 1.0.5

  • Released to CRAN.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("helminthR")

1.0.7 by Tad Dallas, 2 months ago


https://github.com/rOpenSci/helminthR


Report a bug at https://github.com/rOpenSci/helminthR/issues


Browse source code at https://github.com/cran/helminthR


Authors: Tad Dallas


Documentation:   PDF Manual  


GPL-3 license


Imports xml2, rvest, httr, magrittr, plyr, utils, knitr, rmarkdown

Suggests testthat


See at CRAN