| Title: | Access London Natural History Museum Host-Helminth Record Database |
|---|---|
| Description: | Access to large host-parasite data is often hampered by the availability of data and difficulty in obtaining it in a programmatic way to encourage analyses. 'helminthR' provides accesss to the London Natural History Museum's host-parasite database, one of the largest host-parasite databases existing currently. |
| Authors: | Tad Dallas [aut, cre] |
| Maintainer: | Tad Dallas <[email protected]> |
| License: | GPL-3 |
| Version: | 1.1.0 |
| Built: | 2025-06-24 20:27:01 UTC |
| Source: | https://github.com/ropensci/helminthR |
'helminthR': data from the London Natural History Museum's host-parasite database.
Tad Dallas [email protected]
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/
Useful links:
Report bugs at https://github.com/rOpenSci/helminthR/issues/
Given the data or a subset of the helminth interaction data (see 'loadData()'), perform various cleaning functions on the data, including validation of species names, run taxize on hosts (again, as there are already host and parasite taxonomic variables as part of this data.frame , and remove records only to genus level.
cleanData(data, speciesOnly = FALSE, validateHosts = FALSE)cleanData(data, speciesOnly = FALSE, validateHosts = FALSE)
data |
helminth interaction data |
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) |
Use data(locations) for a list of possible locations.
data.frame with cleaned data
Tad Dallas
Load the helminth interaction data
loadData(outdir = ".")loadData(outdir = ".")
outdir |
output directory (default is the top-level of the package repo) |
data.frame of host-helminth interactions
Tad Dallas
Gibson, D. I., Bray, R. A., & Harris, E. A. (Compilers) (2005). Host-Parasite Database of the Natural History Museum, London.
Lists geographic locations and the corresponding latitude and longitude coordinates
of the country's centroid. The georeferencing was performed dynamically using the
Google Maps API, but they have since restricted access. The data on locations is now
provided in this data file called locations – data(locations) – and
is based on an earlier usage of ggmap. The geographic coordinates may not
be accurate, and users should check for accuracy (and feel free to file an issue or
PR on Github with corrections).
data(locations)data(locations)
Name of geographic location
Latitude of location centroid
Longitude of location centroid
Gibson, D. I., Bray, R. A., & Harris, E. A. (Compilers) (2005). Host-Parasite Database of the Natural History Museum, London.