This is an introduction to the
helminthR
package, whicih allows for the programmatic
access to the London Natural History Museum’s helminth parasite database
(available
here). This database represents the largest known database of
host-helminth interactions, containing host-helminth occurrence records
for over 350 locations, including aquatic, marine, and terrestrial
locations.
See software note in Ecography (available here)
From GitHub
From CRAN
The package allows for the acquisition of host-helminth interaction
records based on host name (genus or species), parasite name (genus,
species, or group), and/or location (accepted region name as provided in
data(locations)
. Parasite groups include
“Acanthocephalans”, “Cestodes”, “Monogeans”, “Nematodes”, “Trematodes”,
or “Turbs” (short for Turbellarians). The user can further define host
species as occuring
by inputting the corresponding number above in the
hostState
argument.
The package itself has three main functions; findHost
,
findParasite
, and findLocation
.
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. We also use the
citation
argument here to obtain information on the
citations which the host-helminth occurrences are based on.
gorillaParasites <- findHost(genus='Gorilla', species='gorilla',
hostState=1, speciesOnly=TRUE, citation=TRUE)
The above function will query the database for helminth parasites of Gorilla gorilla that were captured in the wild, and will remove helminth parasites not identified to species. If the user wishes to query multiple host species at the same time, the user can do the following
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.
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.
Below, I provide an example of code for plotting the bipartite network of host-helminth interactions found in the state of Montana.