Guidelines for data reuse and update
Due to the version system of VegVault, the database is expected to be updated using new data and/or changing the process of data migration and processing. Therefore, we recommend citing the latest VegVault version with corresponding DOI.
As the primary data sources are held under various licences, the VegVault has an CC BY-NC-ND 4.0 Licence (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en), allowing the usage of more restricted data (i.e. BIEN data is under CC BY-NC-ND). We recommend users to carefully read the constricts associated with data usage. In addition, when citing the usage of VegVault, users should always cite the primary sources of the data, as well as any individual datasets. For those purposes, we created a function vaulkeeper::get_references() within the {vaultkeepr} R package (see below) that will output a list of recommended references for the specific data compilation created by the user.
Limitations and considerations for future research
Potential limitation lies in the completeness, accuracy, and reliability of the primary data sources. For example, it has been suggested that improper data practices erode the quality of global ecological databases such as TRY38, which have been used in VegVault. We do not attempt to solve these problems as VegVault’s main purpose is the re-usability of the data. Note that for some cases we are not permitted to make modifications based on the original data (e.g. BIEN data has CC BY-NC-ND licence).
{vaultkeeper}: R-package for accessing the VegVault database
In order to make usage of the VegVault database as easy as possible, we have developed an R-package called {vaultkeepr}, providing a suite of functions to effectively interact with the database directly from the R programming language. Functions include opening the database, extracting datasets, filtering samples, and accessing specific taxa and traits. This package is a well-tested interface (>95% code coverage).
The {vaultkeepr} can be installed from GitHub with:
# install.packages("remotes")
remotes::install_github("OndrejMottl/vaultkeepr")and then all functions will be made available by attaching as:
library(vaultkeepr)See Exampe of usage for more details.