ohvbd-package: ohvbd: One Health VBD Hub

In ohvbd: One Health VBD Hub

ohvbd: One Health VBD Hub

Description

Interface with the One Health VBD Hub and related repositories directly.

Introduction

ohvbd is a data location and ingestion package focused around a series of vector-borne disease databases. It aims to make it quick and easy to repeatably download data from a variety of sources without having to navigate online tools and pages.

Searching

ohvbd can be used to search a multitude of databases using the ⁠search_*⁠ family of functions.

Most prominent of these is the search_hub() function, which leverages the <vbdhub.org> search functionality to provide enhanced searches across databases.

# Search hub for the Castor Bean Tick
search_hub("Ixodes ricinus")

Other dedicated search functionality is available for select databases (e.g. search_vt_smart()).

Downloading

Once relevant data has been identified, these can be downloaded using the fetch() function.

This is typically performed using a piped approach:

# Find and retrieve tick data from VecTraits
ixodes_results <- search_hub("Ixodes ricinus", db = "vt") |>
                    fetch()

Parsing & Filtering

Downloaded data is simply stored as the responses from the website.

To use the information itself we must use glean() to extract the relevant data:

# Find and retrieve tick data from VecTraits
ixodes_data <- search_hub("Ixodes ricinus", db = "vt") |>
                 fetch() |>
                 glean()

Associating with other data

Downloaded data can be associated with climatic variables from AREAData using the ⁠assoc_*⁠ functions.

ixodes_data <- search_hub("Ixodes ricinus", "vt") |>
  tail(20) |>
  fetch() |>
  glean(cols = c(
    "DatasetID",
    "Latitude",
    "Longitude",
    "Interactor1Genus",
    "Interactor1Species"
  ), returnunique = TRUE)
areadata <- fetch_ad(metric="temp", gid=0, use_cache=TRUE)
ad_extract_working <- assoc_ad(ixodes_data, areadata,
                               targetdate = c("2021-08-04"),
                               enddate=c("2021-08-06"),
                               gid=0,
                               lonlat_names = c("Longitude", "Latitude"))

Further information

The ohvbd homepage is at https://ohvbd.vbdhub.org. See especially the documentation section. Join the discussion forum at https://forum.vbdhub.org/c/ohvbd-r-package/ if you have questions or comments.

Author(s)

Maintainer: Francis Windram [e-mail] (ORCID) [copyright holder]

See Also

Useful links:

• https://github.com/fwimp/ohvbd

• https://ohvbd.vbdhub.org

• Report bugs at https://github.com/fwimp/ohvbd/issues

ohvbd documentation built on March 10, 2026, 1:07 a.m.