
Introduction to the helminthR package
Tad Dallas
Source:vignettes/helminthR_vignette.Rmd
helminthR_vignette.Rmd
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)
Installation
From GitHub
# install.packages("devtools")
devtools::install_github("rOpenSci/helminthR")
library("helminthR")
From CRAN
install.packages("helminthR")
Package functionality
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
- “In the wild”
- “Zoo captivity”
- “Domesticated”
- “Experimental”
- “Commercial source”
- “Accidental infestation”
by inputting the corresponding number above in the
hostState
argument.
The package itself has two base functions; loadData
and
cleanData
loadData()
This function loads the data. The data were previously served by the London Natural History Museum, so this package programmatically accessed them via API queries. The data have been archived, and this package ships with a zipped copy of the current release of the data.
data <- loadData()
cleanData()
There are numerous records that the end user may want to remove
before analyzing the data. For instance, (Deer)
is a valid
host species listed, as is (duck)
. We can clean the data to
remove these records and others not identified to species-level, as well
as use taxize
to access taxonomic data on hosts using the
cleanData()
function.
data2 <- cleanData(data)
data(locations)
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 used to subset the existing
data product (see loadData()
). Below, I look at
host-parasite associations recorded in France.