Summary

The R Modular Analysis of Vegetation Information System (RMAVIS) is a R Shiny application for the assignment of vegetation sample plot data to the British National Vegetation Classification (GB-NVC) and the Minnesota Native Plant Community Classification (MNNPC).

RMAVIS is the latest in a series of computer programs for NVC assignment, beginning with TABLEFIT, then MATCH, and most recently MAVIS - for which it is the successor.

At present RMAVIS provides the following functionality:

  • Calculate similarities and assign vegetation sample plot data to GB NVC communities, with a new set of Scottish oceanic wet grassland communities provided by the Floodplain Meadows Partnership.
  • Retrieve the habitats associated with the top-fitting NVC communities from alternative habitat classifications.
  • Composes floristic tables from the survey data and views the NVC floristic tables side-by-side.
  • Compiles a frequency table containing the occurrence of each species present in the vegetation sample plots over time.
  • Calculates mean environmental indicator values, at present the Hill-Ellenberg moisture, light, nitrogen, reaction, and salinity scores.
  • Calculates a range of diversity metrics.
  • Performs a multivariate analysis, facilitating the visualisation of the sample plots in an ordination space.
  • Provides the facility to download the results of an RMAVIS session as a xlsx file or generate a pdf report.

 

Accessing RMAVIS

RMAVIS is hosted on the UKCEH Posit Connect server.

Access RMAVIS

 

Feedback

Feedback on RMAVIS is welcome and can be submitted via a form, by creating a Github issue, or by contacting Zeke Marshall.

Feedback form

Github issue

 

Recommended citation

Paper

To reference RMAVIS please cite the JOSS paper as follows:

Marshall et al., (2024). RMAVIS v1.0: a Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities. Journal of Open Source Software, 9(100), 6682, https://doi.org/10.21105/joss.06682

DOI

 

Code

The code which constitutes RMAVIS is stored and versioned using Zenodo. Cite all versions of the RMAVIS code as follows:

Marshall, Z., Smart, S. M., Harrower, C., & Marrs, R. (2024). RMAVIS. Zenodo. https://zenodo.org/doi/10.5281/zenodo.10818640

DOI

Alternatively, to cite a particular version of RMAVIS retrieve the citation information from that Zenodo release.

Acknowledgements

The initial development of `RMAVIS` was partly supported by the UK‐SCAPE delivering National Capability (NE/R016429/1) programme.
The integration of the MNNPC into RMAVIS was partly supported by the UKCEH National Capability for UK Challenges (NE/Y006208/1) programme funded by the Natural Environment Research Council (Zeke Marshall) and the Minnesota Environment and Natural Resources Trust Fund as recommended by the Legislative-Citizen Commission on Minnesota Resources (LCCMR) (Amy Kendig).

Special thanks are given to Colin Conroy and Barry Jobson for their ongoing and essential support testing RMAVIS.