One Health VBD Hub

Interface with the One Health VBD (vector-borne disease) Hub < https://vbdhub.org/> and related repositories (VectorByte < https://www.vectorbyte.org>, GBIF < https://www.gbif.org> and AREAdata < https://pearselab.github.io/areadata/>) directly to find, download, and subset vector-borne disease data.

One Health VBD Hub (ohvbd)

Introduction

ohvbd is an R package for retrieving (and parsing) data from a network of disease vector data sources.

This package was developed as part of the One Health Vector-Borne Diseases Hub.

Databases

ohvbd allows for searching and the retrieval of data from the following data sources:

vbdhub (search only)
VecTraits
VecDyn
GBIF
AreaData

Installation

You can install the stable version of ohvbd from CRAN:

install.packages("ohvbd")

You can alternatively install the development version of ohvbd from GitHub including any new or experimental features:

# install.packages("devtools")
devtools::install_github("fwimp/ohvbd")

The vignettes are all available online, but if you would like to build them locally, add build_vignettes = TRUE into your install_github() command. However, we do not recommend doing this due to the number of extra R packages utilised in the vignettes.

Basic usage

ohvbd has been designed to make finding and retrieving data on disease vectors simple and straightforward.

Typically it uses a “piped”-style approach to find, get, and filter data from the supported databases, however it aims to provide the data to you “as-is”, leaving further downstream analysis and filtering down to you.

A basic pipeline for finding and retrieving data on Ixodes ricinus from the VecTraits database looks something like this:

library(ohvbd)

df <- search_hub("Ixodes ricinus") |>
  filter_db("vt") |>
  fetch() |>
  glean()

Latest release patch notes

ohvbd 1.0.1

ohvbd now explicitly depends on generics (as it does anyway via lubridate). This should stop issues loading the package after install.
search_hub() now correctly interfaces with the output of match_countries() even when onlywkt is not provided.

See changelog for patch notes for all versions.