findLocation {helminthR}

Find host-parasite interactions for a given location

Description

Given a location (available from data{locations}) this function returns all host-parasite associations in that location.

Usage

findLocation(
  location = NULL,
  group = NULL,
  citation = FALSE,
  hostState = NULL,
  speciesOnly = FALSE,
  validateHosts = FALSE,
  removeDuplicates = FALSE
)

Arguments

location

Location of host-parasite interaction.

group

Parasite group - Cestodes, Acanthocephalans, Monogeneans, Nematodes, Trematodes, or Turbellarian etc. (Turb)

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)

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"

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

findHost

Examples

 FrenchHostPars <- helminthR::findLocation(location="France")