Joins host-level parasite summaries from the Global Mammal Parasite Database
(Stephens et al. 2017) to a taxify() result by looking up accepted_name.
The database's host-parasite association records are aggregated to one row per
host species.
Arguments
- x
A data.frame returned by
taxify().- cols
Which columns to attach:
NULL(default) the curated set,"all"every column the source carries, or a character vector of names. Seeenrichment_cols.- verbose
Logical. Default
TRUE.
Value
The same data.frame with additional columns. The default set:
- gmpd_parasite_richness
Distinct parasite species recorded for the host.
- gmpd_n_helminth, gmpd_n_virus, gmpd_n_bacteria, gmpd_n_protozoa, gmpd_n_arthropod, gmpd_n_fungus, gmpd_n_prion
Distinct parasite species by parasite type.
- gmpd_mean_prevalence
Mean reported prevalence across the host's records.
- gmpd_host_group
Host group (carnivores, ungulates, primates).
Details
Covers wild carnivores, ungulates and primates (462 host species).
Parasite richness is a sampling-sensitive count: a well-studied host accumulates more recorded parasites than a rarely sampled one, so the values reflect research effort as well as biology.
This source states no licence – it is distributed under the journal's
version-of-record terms with a citation request – so taxify ships no
pre-built copy of it. The first call builds it from the original source on
your own machine, which requires the taxifydb package
(remotes::install_github("gcol33/taxifydb")). taxify redistributes none of
the data. Cite Stephens et al. (2017) when you use it.
References
Stephens PR, Pappalardo P, Huang S, et al. (2017) Global Mammal Parasite Database version 2.0. Ecology 98:1476. doi:10.1002/ecy.1799
Examples
if (FALSE) { # \dontrun{
# Builds the enrichment on first use (needs taxifydb).
taxify("Panthera leo", backbone = "gbif") |>
add_gmpd()
} # }