RMAVIS v1.0

RMAVIS v1.0: a Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities - Published in JOSS (2024)

https://github.com/nerc-ceh/rmavis

Repository

A R Shiny application for the assignment of vegetation survey plot data to GB NVC communities with additional exploratory analyses.

README.Rmd

---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# RMAVIS


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## Overview

The **R** **M**odular **A**nalysis of **V**egetation **I**nformation **S**ystem 
(`RMAVIS`) R Shiny web application is a tool to assist in the assignment of 
vegetation plot sample data to GB National Vegetation Classification units,
with additional exploratory analyses.

We will update and improve `RMAVIS` over time in response to user feedback and hope it acts as a useful
tool for the GB ecology and conservation community.

## Structure

There are 8 main sections in `RMAVIS` at present.

**Home** - Provides outlining information.

**Data Entry** - Facilitates data entry and makes available the taxonomic information used by `RMAVIS`.

**NVC Analysis** - The core of the `RMAVIS` application, containing the functionality present in the original v1.0 release.

**NVC Information** - Contains a set of searchable tables for inspecting the NVC community names, taxon names, floristic tables, and community attributes.

**Documentation** - Provides a more detailed overview of the underlying methods, data sources, and usage instructions.

**News** - Contains the release log and additional news regarding the development and maintenance of `RMAVIS`.

**Additional Information** - Contains other useful information.

**Privacy** - A privacy notice.

## Running Locally

In addition to accessing `RMAVIS` via the web `RMAVIS` can be run on your personal device and installed as an R package.

To run RMAVIS locally take the following steps.

1.  Ensure R >= 4.4 is installed.
2.  Install `RMAVIS` using `remotes::install_github("NERC-CEH/RMAVIS")`
3.  Run `install.packages("tinytex")` then `tinytex::install_tinytex()` to install a minimal LaTeX distribution.
    This is required to generate a pdf report.
    Note that this is only required if you do not have a LaTeX distribution already installed.
4.  From the R terminal run `RMAVIS::runApp()`.

If you wish to use the NVC-matching functions outside of the `RMAVIS` app, 
these are also made available through the `RMAVIS` package.

## Reccomended Citation

To reference the core `RMAVIS` application 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,


To cite a specific version of RMAVIS select the relevant release from Zenodo [here](https://zenodo.org/search?q=parent.id%3A10818640&f=allversions%3Atrue&l=list&p=1&s=10&sort=version).

## Feedback

To report a bug please submit a Github issue [here](https://github.com/NERC-CEH/RMAVIS/issues), 
fill out the feedback form [here](https://forms.office.com/e/ByLgRPjT8J), 
or send an email to [Zeke Marshall](mailto:zekmar@ceh.ac.uk?subject=RMAVIS).

## Acknowledgements
The development of this app was partly supported by the UK‐SCAPE 
programme delivering National Capability (NE/R016429/1) funded by the 
Natural Environment Research Council.

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

We would also like to thank Lindsay Maskell, Lucy Ridding, Andy McMullen, John Handley, 
Michael Tso, Simon Rolph, Cristina Martin Hernandez, and George Linney for testing RMAVIS.

Lastly, we would also like to thank Rob Marrs for his ongoing collaboration 
with the development of NVC assignment methodologies and the 
University of Liverpool for their ongoing support.

Owner

JOSS Publication

RMAVIS v1.0: a Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities

Published

August 07, 2024

DOI

10.21105/joss.06682

Volume 9, Issue 100, Page 6682

Authors

Zeke Marshall
UK Centre for Ecology \& Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, United Kingdom

Simon Mark Smart
UK Centre for Ecology \& Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, United Kingdom

Colin Harrower
UK Centre for Ecology \& Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, United Kingdom

Rob Marrs
School of Environmental Sciences, University of Liverpool, Liverpool, L69 3GP, UK

Editor

Michael Mahoney

Tags

Vegetation science NVC Ecology Survey

View PDF Review Thread Software Archive

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use this software, please cite our article in the Journal of Open Source Software
doi: 10.5281/zenodo.10818640
repository-code: 'https://github.com/NERC-CEH/RMAVIS'
license: LGPL-3.0
version: v1.1.3
type: software
authors:
  - given-names: Zeke
    family-names: Marshall
    email: zekmar@ceh.ac.uk
    affiliation: UKCEH
    orcid: 'https://orcid.org/0000-0001-9260-7827'
  - given-names: Simon Mark
    family-names: Smart
    email: ssma@ceh.ac.uk
    affiliation: UKCEH
    orcid: 'https://orcid.org/0000-0003-2750-7832'
  - given-names: Colin
    family-names: Harrower
    email: corr@ceh.ac.uk
    affiliation: UKCEH
    orcid: 'https://orcid.org/0000-0001-5070-5293'
  - given-names: Rob
    family-names: Marrs
    email: calluna@liverpool.ac.uk
    affiliation: University of Liverpool
    orcid: 'https://orcid.org/0000-0002-0664-9420'
abstract: 'A Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities.'
keywords:
  - Vegetation science
  - NVC
  - Ecology
  - Survey
title: "RMAVIS"
preferred-citation:
  authors:
  - family-names: Marshall
    given-names: Zeke
    orcid: "https://orcid.org/0000-0001-9260-7827"
  - family-names: Smart
    given-names: Simon Mark
    orcid: "https://orcid.org/0000-0003-2750-7832"
  - family-names: Harrower
    given-names: Colin
    orcid: "https://orcid.org/0000-0001-5070-5293"
  - family-names: Marrs
    given-names: Rob
    orcid: "https://orcid.org/0000-0002-0664-9420"
  date-published: 2024-08-07
  doi: 10.21105/joss.06682
  issn: 2475-9066
  issue: 100
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6682
  title: "RMAVIS v1.0: a Shiny application for the analysis of
    vegetation survey data and assignment to GB NVC communities."
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06682"
  volume: 9

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