PLEASE NOTE: vegtaxon 2.0 is currently under development and will be released soon. This update will expand the capabilities of the package by including more species and indicators. It will also provide extensive worked through examples.
Developing models that include data from different sources is becoming an increasingly useful method in vegetation ecology. Methodological problems arise when integrating plant species lists compiled from different sources due to taxonomic changes. Accounting for these issues can be time consuming and necessitate the involvement of taxonomic experts. As part of a project integrating four long-term UK vegetation datasets (Countryside Survey, Environmental Change Network, Long Term Monitoring Network, and National Plant Monitoring Scheme) we have developed vegtaxon, an R package created to assist with the harmonisation of vegetation survey data from UK datasets. vegtaxon greatly reduces the time needed to process these data, allowing researchers to spend more time on analysis and interpretation. We hope this will encourage increased utilisation and integration of these datasets. We provide guidance on how to incorporate additional species lists into the package to allow integrated exploration with other datasets.
The values for CSM positives and negatives are currently of limited use for users outside of our UKCEH Integrated Modelling project. These values represent an aggregated value for CSM positive or negative for the following habitats: Lowland dry heath, Lowland raised bog and lowland blanket bog, Alpine dwarf-shrub heath, Upland blanket bog and valley bog. We aim to include CSM positive and negative indicator values for all habitats in further package updates.
You can install vegtaxon from https://github.com/NERC-CEH/vegtaxon with:
devtools::install_github("https://github.com/NERC-CEH/vegtaxon")To access and download data from the Countryside Survey, Environmental Change Network, or National Plant Monitoring Scheme, please go to https://eidc.ac.uk/.
To access and download data from the Natural England Long Term Monitoring Network, please go to http://publications.naturalengland.org.uk/category/5316639066161152.
In some instances, you may use the ext_join() function and find that some of your species names do not match up to those in our database. Should this happen, it may be possible to work through a similar name matching process to the one we used to create the data underpinning this package. This involves the use of the ‘Taxon name parser’ tool provided by the BSBI. To access this, users must request access to the BSBI Distribution Database (see https://database.bsbi.org/). We are currently updating the full documentation for this workflow, and aim to have it uploaded here in early 2021. In the short term, do get in touch if this is something you are interested in. I am happy to have a discussion and provide draft guidance.