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