Version 0.9991

NERC-CEH · Apr 17, 2024 · 04a5c5b · 04a5c5b
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diff --git a/CITATION.cff b/CITATION.cff
@@ -23,6 +23,11 @@ authors:
     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'
 repository-code: 'https://github.com/ZekeMarshall/RMAVIS'
 abstract: 'A R Shiny application for the assignment of vegetation survey plot data to GB NVC communities with additional exploratory analyses.'
 keywords:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: RMAVIS
 Title: Assign Vegetation Survey Data to GB NVC Communities
-Version: 0.999
-Date: 2024-04-16
+Version: 0.9991
+Date: 2024-04-17
 Authors@R: c(person(given = "Zeke",
                     family = "Marshall",
                     role = c("aut", "cre"),
@@ -16,7 +16,12 @@ Authors@R: c(person(given = "Zeke",
                     family = "Harrower", 
                     email = "corr@ceh.ac.uk", 
                     role = c("aut"),
-                    comment = c(ORCID = "0000-0001-5070-5293")))
+                    comment = c(ORCID = "0000-0001-5070-5293"))
+             person(given = "Rob", 
+                    family = "Marrs", 
+                    email = "calluna@liverpool.ac.uk", 
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0002-0664-9420")))
 Description: A R Shiny application for the assignment of vegetation survey plot data to GB NVC communities with additional exploratory analyses.
 License: MIT + file LICENSE
 Encoding: UTF-8

diff --git a/JOSS/paper.Rmd b/JOSS/paper.Rmd
@@ -15,11 +15,16 @@ authors:
   - name: Colin Harrower
     orcid: 0000-0001-5070-5293
     affiliation: 2
+  - name: Rob Marrs
+    orcid: 0000-0002-0664-9420
+    affiliation: 3
 affiliations:
   - name: UK Centre for Ecology \& Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, United Kingdom
     index: 1
   - name: UK Centre for Ecology \& Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, United Kingdom
     index: 2
+  - name: School of Environmental Sciences, University of Liverpool, Liverpool, L69 3GP, UK
+    index: 3
 date: "`r Sys.Date()`"
 bibliography: paper.bib
 output:

diff --git a/JOSS/paper.html b/JOSS/paper.html
@@ -10,7 +10,7 @@
 
 
 
-<meta name="date" content="2024-04-15" />
+<meta name="date" content="2024-04-17" />
 
 <title>RMAVIS v1.0: a R Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities.</title>
 
@@ -374,7 +374,7 @@
 <h1 class="title toc-ignore"><code>RMAVIS</code> v1.0: a R Shiny
 application for the analysis of vegetation survey data and assignment to
 GB NVC communities.</h1>
-<h4 class="date">2024-04-15</h4>
+<h4 class="date">2024-04-17</h4>
 
 </div>
 

diff --git a/JOSS/paper.md b/JOSS/paper.md
@@ -15,12 +15,17 @@ authors:
   - name: Colin Harrower
     orcid: 0000-0001-5070-5293
     affiliation: 2
+  - name: Rob Marrs
+    orcid: 0000-0002-0664-9420
+    affiliation: 3
 affiliations:
   - name: UK Centre for Ecology \& Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, United Kingdom
     index: 1
   - name: UK Centre for Ecology \& Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, United Kingdom
     index: 2
-date: "2024-04-15"
+  - name: School of Environmental Sciences, University of Liverpool, Liverpool, L69 3GP, UK
+    index: 3
+date: "2024-04-17"
 bibliography: paper.bib
 output:
   html_document:

diff --git a/NEWS.md b/NEWS.md
@@ -3,6 +3,13 @@ title: "Release notes for `RMAVIS`"
 output: html_document
 ---
 
+# RMAVIS 0.9991 (2024-04-17)
+*   Modifications:
+      -   Updating author list.
+*   Fixes: NA
+*   New Features: NA
+
+
 # RMAVIS 0.999 (2024-04-16)
 *   Modifications:
       -   Updating to taxonomic backbone to use BSBI February 2024 taxon list.

diff --git a/README.Rmd b/README.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
 # RMAVIS
 
 <!-- badges: start -->
-[![Generic badge](https://img.shields.io/badge/Version-0.999-green.svg)]()
+[![Generic badge](https://img.shields.io/badge/Version-0.9991-green.svg)]()
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![DOI](https://zenodo.org/badge/722095560.svg)](https://zenodo.org/badge/latestdoi/722095560)
 [![status](https://joss.theoj.org/papers/460c6f934a108fcf5a16d0f2ab77492e/status.svg)](https://joss.theoj.org/papers/460c6f934a108fcf5a16d0f2ab77492e)

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 <!-- badges: start -->
 
 [![Generic
-badge](https://img.shields.io/badge/Version-0.999-green.svg)]()
+badge](https://img.shields.io/badge/Version-0.9991-green.svg)]()
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
 developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

diff --git a/docs/documentation.Rmd b/docs/documentation.Rmd
@@ -1,6 +1,6 @@
 ---
 title: "RMAVIS - Documentation"
-subtitle: "v0.999"
+subtitle: "v0.9991"
 # output:
 #   bookdown::word_document2:
 # always_allow_html: true
@@ -132,6 +132,7 @@ This option is included to ensure that users who cannot confidently identify
 bryophytes to the species rank, or do not have data where bryophytes
 were confidently recorded can still use RMAVIS without
 false presences or absences unduly skewing the results.
+
 > Caution is advised in excluding bryophyte taxa as bryophytes are key and often
 > highly diagnostic components of many NVC communities.
 

diff --git a/report/Report.Rmd b/report/Report.Rmd
@@ -149,7 +149,7 @@ reportOptions_options <- list(`NVC Assignment` = c("Site, Czekanowski" = "nvcAss
 
 ```{r RMAVISVersion, echo=FALSE, message=FALSE, warning=FALSE, results='asis'}
 
-cat("**Version:** ", as.character("v0.999"), sep = "")
+cat("**Version:** ", as.character("v0.9991"), sep = "")
 
 ```
 

diff --git a/www/documentation.html b/www/documentation.html
@@ -1711,7 +1711,7 @@
 
 
 <h1 class="title toc-ignore">RMAVIS - Documentation</h1>
-<h3 class="subtitle">v0.999</h3>
+<h3 class="subtitle">v0.9991</h3>
 
 </div>
 
@@ -1782,9 +1782,11 @@ <h3><span class="header-section-number">2.1.1</span> Options</h3>
 This option is included to ensure that users who cannot confidently identify
 bryophytes to the species rank, or do not have data where bryophytes
 were confidently recorded can still use RMAVIS without
-false presences or absences unduly skewing the results.
-&gt; Caution is advised in excluding bryophyte taxa as bryophytes are key and often
-&gt; highly diagnostic components of many NVC communities.</p>
+false presences or absences unduly skewing the results.</p>
+<blockquote>
+<p>Caution is advised in excluding bryophyte taxa as bryophytes are key and often
+highly diagnostic components of many NVC communities.</p>
+</blockquote>
 <p><strong>Input Method</strong></p>
 <p>Three methods for entering data into <code>RMAVIS</code> are provided: manual, upload,
 and example. The manual method allows the user to enter the data
-Original file line number
+Diff line change
@@ Expand Up @@
     ```{r RMAVISVersion, echo=FALSE, message=FALSE, warning=FALSE, results='asis'}
-    cat("**Version:** ", as.character("v0.999"), sep = "")
+    cat("**Version:** ", as.character("v0.9991"), sep = "")
     ```
@@ Expand Down @@