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)
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.
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.
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/>
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])})
#> Host Parasite
#> 1 Gorilla gorilla Strongyle
#> 2 Gorilla gorilla beringei Strongyle
#> 3 Gorilla gorilla Strongyloidea
#> 4 Gorilla gorilla Trichostrongylidae
#> 5 Gorilla gorilla Anoplocephala gorillae
#> 6 Gorilla gorilla beringei Anoplocephala gorillae
#> 7 Gorilla gorilla graueri Anoplocephala gorillae
#> 8 Gorilla gorilla beringei Anoplocephala sp.
#> 9 Gorilla gorilla Brodenia jonchi
#> 10 Gorilla gorilla beringei Capillaria hepatica
#> 11 Gorilla gorilla Echinococcus multilocularis
#> 12 Gorilla gorilla Gongylonema sp.
#> 13 Gorilla gorilla Hyostrongylus kigeziensis
#> 14 Gorilla gorilla beringei Hyostrongylus kigeziensis
#> 15 Gorilla gorilla beringei Hyostrongylus sp.
#> 16 Gorilla gorilla Loa loa
#> 17 Gorilla gorilla Mansonella perstans
#> 18 Gorilla gorilla Mansonella sp.
#> 19 Gorilla gorilla Mansonella streptocerca
#> 20 Gorilla gorilla Mansonella Esslingeria
#> 21 Gorilla gorilla Mansonella Esslingeria
#> 22 Gorilla gorilla Murshidia sp.
#> 23 Gorilla gorilla beringei Murshidia sp.
#> 24 Gorilla gorilla Oesophagostomum sp.
#> 25 Gorilla gorilla beringei Oesophagostomum sp.
#> 26 Gorilla gorilla graueri Oesophagostomum stephanostomum
#> 27 Gorilla gorilla Onchocerca volvulus
#> 28 Gorilla gorilla Paralibyostrongylus kalinae
#> 29 Gorilla gorilla beringei Paralibyostrongylus kalinae
#> 30 Gorilla gorilla Probstmayria gabonensis
#> 31 Gorilla gorilla Probstmayria goodallae
#> 32 Gorilla gorilla beringei Probstmayria sp.
#> 33 Gorilla gorilla graueri Probstmayria spp.
#> 34 Gorilla gorilla beringei Strongyloides fuelleborni
#> 35 Gorilla gorilla graueri Strongyloides fuelleborni
#> 36 Gorilla gorilla beringei Strongyloides sp.
#> 37 Gorilla gorilla Strongyloides sp.
#> 38 Gorilla gorilla Strongyloides spp.
#> 39 Gorilla gorilla beringei Trichostrongylus sp.
#> 40 Gorilla gorilla beringei Trichuris trichiura
#> 41 Peromyscus leucopus leucopus Alaria mustelae
#> 42 Peromyscus leucopus noveboracensis Alaria mustelae
#> 43 Peromyscus leucopus Baylisascaris procyonis
#> 44 Peromyscus leucopus Brachylaima peromysci
#> 45 Peromyscus leucopus leucopus Brachylaima peromysci
#> 46 Peromyscus leucopus leucopus Brachylaima thompsoni
#> 47 Peromyscus leucopus noveboracensis Brachylaima thompsoni
#> 48 Peromyscus leucopus Brachylaima virginianum
#> 49 Peromyscus leucopus noveboracensis Brachylaima virginianum
#> 50 Peromyscus leucopus Capillaria hepatica
#> 51 Peromyscus leucopus noveboracensis Capillaria hepatica
#> 52 Peromyscus leucopus Euryhelmis squamula
#> 53 Peromyscus leucopus Hymenolepis bennetti
#> 54 Peromyscus leucopus Hymenolepis citelli
#> 55 Peromyscus leucopus Physaloptera sp.
#> 56 Peromyscus leucopus Rictularia coloradensis
#> 57 Peromyscus leucopus Schistosomatium douthitti
#> 58 Peromyscus leucopus Syphacia Seuratoxyuris
#> 59 Peromyscus leucopus Taenia multiceps
#> 60 Peromyscus leucopus Taenia mustelae
#> 61 Peromyscus leucopus Trichinella spiralis
#> ParasiteFull
#> 1 (Strongyle)
#> 2 (Strongyle)
#> 3 (Strongyloidea)
#> 4 (Trichostrongylidae)
#> 5 Anoplocephala gorillae Nybelin, 1928
#> 6 Anoplocephala gorillae Nybelin, 1928
#> 7 Anoplocephala gorillae Nybelin, 1928
#> 8 Anoplocephala sp.
#> 9 Brodenia jonchi Gallego Berenguer, Selva Valdespinosa & Esteban Fernandez, 1965
#> 10 Capillaria hepatica (Bancroft, 1893)
#> 11 Echinococcus multilocularis Leuckart, 1863
#> 12 Gongylonema sp.
#> 13 Hyostrongylus kigeziensis Durette-Desset et al., 1992
#> 14 Hyostrongylus kigeziensis Durette-Desset et al., 1992
#> 15 Hyostrongylus sp.
#> 16 Loa loa (Guyot, 1778)
#> 17 Mansonella perstans (Manson, 1891)
#> 18 Mansonella sp.
#> 19 Mansonella streptocerca
#> 20 Mansonella (Esslingeria) leopoldi (Berghe, Peel & Chardome, 1957)
#> 21 Mansonella (Esslingeria) lopeensis Bain, Moisson, Huerre, Landsoud-Soukate & Tutin, 1995
#> 22 Murshidia sp.
#> 23 Murshidia sp.
#> 24 Oesophagostomum sp.
#> 25 Oesophagostomum sp.
#> 26 Oesophagostomum stephanostomum Railliet & Henry, 1909
#> 27 Onchocerca volvulus (Leuckart in Mans., 1893)
#> 28 Paralibyostrongylus kalinae Durette-Desset et al., 1992
#> 29 Paralibyostrongylus kalinae Durette-Desset et al., 1992
#> 30 Probstmayria gabonensis Waerebeke et al., 1988
#> 31 Probstmayria goodallae Waerebeke et al., 1988
#> 32 Probstmayria sp.
#> 33 Probstmayria spp.
#> 34 Strongyloides fuelleborni Linstow, 1905
#> 35 Strongyloides fuelleborni Linstow, 1905
#> 36 Strongyloides sp.
#> 37 Strongyloides sp. (cf. fuelleborni)
#> 38 Strongyloides spp.
#> 39 Trichostrongylus sp.
#> 40 Trichuris trichiura (Linnaeus, 1771)
#> 41 Alaria mustelae Bosma, 1931
#> 42 Alaria mustelae Bosma, 1931
#> 43 Baylisascaris procyonis (Stefanski & Zarnowski, 1951)
#> 44 Brachylaima peromysci Reynolds, 1938
#> 45 Brachylaima peromysci Reynolds, 1938
#> 46 Brachylaima thompsoni (Sinitsin, 1931)
#> 47 Brachylaima thompsoni (Sinitsin, 1931)
#> 48 Brachylaima virginianum (Dickerson, 1930)
#> 49 Brachylaima virginianum (Dickerson, 1930)
#> 50 Capillaria hepatica (Bancroft, 1893)
#> 51 Capillaria hepatica (Bancroft, 1893)
#> 52 Euryhelmis squamula (Rudolphi, 1819)
#> 53 Hymenolepis bennetti
#> 54 Hymenolepis citelli McLeod, 1933
#> 55 Physaloptera sp.
#> 56 Rictularia coloradensis Hall, 1916
#> 57 Schistosomatium douthitti (Cort, 1915)
#> 58 Syphacia (Seuratoxyuris) peromysci Harkema, 1936
#> 59 Taenia multiceps Leske, 1780
#> 60 Taenia mustelae Gmelin, 1790
#> 61 Trichinella spiralis (Owen, 1835)