findHost {helminthR} | R Documentation |
Find parasite occurrence data for given host.
Description
Given a host genus, species, and/or location, returns a list of parasite
occurrences on that host or for that location.
Use data(locations)
for a list of possible locations.
Usage
findHost(
genus = NULL,
species = NULL,
location = NULL,
citation = FALSE,
hostState = NULL,
speciesOnly = FALSE,
validateHosts = FALSE,
parGroup = NULL,
removeDuplicates = FALSE
)
Arguments
genus |
Host genus |
species |
Host species |
location |
Geographic location. |
citation |
Boolean. Should the output include the citation link and the number of supporting citations? default is FALSE |
hostState |
number corresponding to one of six different host states. The default value is NULL and includes all host states |
speciesOnly |
boolean flag to remove host and parasite species where data are only available at genus level (default = FALSE) |
validateHosts |
boolean flag to check host species names against Catalogue of Life information and output taxonomic information (default = FALSE) |
parGroup |
name of parasite group to query (default queries all groups) |
removeDuplicates |
(boolean) should duplicate host-parasite combinations be removed? (default is FALSE) |
Details
hostState
can take values 1-6 corresponding to if the recorded host
was found
(1) "In the wild"
(2) "Zoo captivity"
(3) "Domesticated"
(4) "Experimental"
(5) "Commercial source"
(6) "Accidental infestation"
A value of NULL should be entered if you would like to include all hostStates.
parGroup
can be specified as "Acanthocephalans", "Cestodes",
"Monogeans", "Nematodes", "Trematodes", or "Turbs" (Turbellarians etc.).
The default is to query all helminth parasite taxa.
Value
Three (or five) column data.frame containing host species, parasite species (shortened name and full name), and citation link and number of citations (if 'citation'=TRUE), with each row corresponding to an occurrence of a parasite species on a host species.
Author(s)
Tad Dallas
References
Gibson, D. I., Bray, R. A., & Harris, E. A. (Compilers) (2005). Host-Parasite Database of the Natural History Museum, London. <http://www.nhm.ac.uk/research-curation/scientific-resources/taxonomy-systematics/host-parasites/>
See Also
Examples
gorillaParasites <- helminthR::findHost("Gorilla", "gorilla")
# An example of how to query multiple hosts when you have a
# vector of host species names
hosts <- c("Gorilla gorilla", "Peromyscus leucopus")
plyr::ldply(hosts, function(x)
{helminthR::findHost(unlist(strsplit(x, " "))[1], unlist(strsplit(x," "))[2])})