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 development version of ohvbd from GitHub with:

# 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 0.6.1

New search_hub() function enables searching across multiple databases at once via vbdhub.
- This includes new functionality for specifying searches using spatial extent polygons and generally more intelligent search behaviour.
New function generate_vt_template() which quickly generates a VecTraits template for later upload.