findHost: Find parasite occurrence data for given host.

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/findHost.R

Description

Given a host genus, species, and/or location, returns a list of parasite occurrences on that host or for that location. Search available locations using the listLocations function.

Usage

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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

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

findParasite

Examples

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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])})

ropensci/helminthR documentation built on Sept. 30, 2018, 6:28 p.m.