Version 0.999

NERC-CEH · Apr 16, 2024 · b233b2e · b233b2e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: RMAVIS
 Title: Assign Vegetation Survey Data to GB NVC Communities
-Version: 1.0
-Date: 2024-04-15
+Version: 0.999
+Date: 2024-04-16
 Authors@R: c(person(given = "Zeke",
                     family = "Marshall",
                     role = c("aut", "cre"),

diff --git a/JOSS/paper.Rmd b/JOSS/paper.Rmd
@@ -122,7 +122,7 @@ charophyte (*Charophyta*) taxa, along with one unspecified 'algae' taxon present
 in the NVC floristic tables.
 The NVC communities present in `RMAVIS` are composed from @rodwell1991, 
 @rodwell1992, @rodwell1992a, @rodwell1995, @rodwell2000, 
-@wallace2017, and @prosser2023.
+@wallace2017, @prosser2023, and @wallace2023.
 Data for habitat correspondences is derived from: 
 the Joint Nature Conservation Committee (JNCC) Spreadsheet of Habitat 
 Correspondences [@jncc2008],

diff --git a/JOSS/paper.bib b/JOSS/paper.bib
@@ -393,6 +393,15 @@ @unpublished{wallace2018
   url       = {http://nora.nerc.ac.uk/id/eprint/524094/}
 }
 
+@article{wallace2023,
+  title   = {An Exploration of Oceanic Wet Grasslands in the {{Scottish}} Coastal Lowlands},
+  author  = {Wallace, Hilary and Gowing, David and Lawson, Clare and Rothero, Emma and Strachan, Ian},
+  year    = {2023},
+  month   = dec,
+  journal = {British Wildlife},
+  url     = {https://www.britishwildlife.com/article/article-volume-35-number-3-page-193-200/}
+}
+
 @article{wood2015,
   title     = {Woodland Survey of Great Britain 1971-2001},
   volume    = {7},

diff --git a/JOSS/paper.html b/JOSS/paper.html
@@ -10,7 +10,7 @@
 
 
 
-<meta name="date" content="2024-04-13" />
+<meta name="date" content="2024-04-15" />
 
 <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">2024-04-13</h4>
+<h4 class="date">2024-04-15</h4>
 
 </div>
 
@@ -540,9 +540,9 @@ <h1>Data sources</h1>
 present in the NVC floristic tables. The NVC communities present in
 <code>RMAVIS</code> are composed from <span class="citation">Rodwell
 (1991)</span>, <span class="citation">Rodwell (1992a)</span>, <span class="citation">Rodwell (1992b)</span>, <span class="citation">Rodwell
-(1995)</span>, <span class="citation">Rodwell (2000)</span>, <span class="citation">Wallace and Prosser (2017)</span>, and <span class="citation">Prosser, Wallace, and Gowing (2023)</span>. Data for
-habitat correspondences is derived from: the Joint Nature Conservation
-Committee (JNCC) Spreadsheet of Habitat Correspondences <span class="citation">(JNCC 2008)</span>, UKHab V1.1 <span class="citation">(Butcher et al. 2020)</span>, and the National Plant
+(1995)</span>, <span class="citation">Rodwell (2000)</span>, <span class="citation">Hillary Wallace and Prosser (2017)</span>, <span class="citation">Prosser, Wallace, and Gowing (2023)</span>, and <span class="citation">Hilary Wallace et al. (2023)</span>. Data for habitat
+correspondences is derived from: the Joint Nature Conservation Committee
+(JNCC) Spreadsheet of Habitat Correspondences <span class="citation">(JNCC 2008)</span>, UKHab V1.1 <span class="citation">(Butcher et al. 2020)</span>, and the National Plant
 Monitoring Scheme (NPMS) habitat correspondences <span class="citation">(Pescott et al. 2019)</span>. Data for the vascular
 plant Hill-Ellenberg values were retrieved from the BSBI checklists,
 specifically the Nitrogen Score (N) <span class="citation">(BSBI
@@ -556,8 +556,8 @@ <h1>Data sources</h1>
 Down <span class="citation">(Ridding et al. 2020)</span>, 2) Leith Hill
 Place Wood <span class="citation">(Wood, Smart, and Bunce 2015; Smart et
 al. 2024)</span>, 3) Whitwell Common <span class="citation">(Smart
-2000)</span>, and 4) Newborough Warren <span class="citation">(Wallace
-and Jones 2018)</span>.</p>
+2000)</span>, and 4) Newborough Warren <span class="citation">(Hillary
+Wallace and Jones 2018)</span>.</p>
 </div>
 <div id="conclusion" class="section level1">
 <h1>Conclusion</h1>
@@ -771,6 +771,12 @@ <h1 class="unnumbered">References</h1>
 Ecosystems Quality and Their Dynamics from Reference Conditions.”</span>
 <em>Ecosphere</em> 14 (12): e4726. <a href="https://doi.org/10.1002/ecs2.4726">https://doi.org/10.1002/ecs2.4726</a>.
 </div>
+<div id="ref-wallace2023" class="csl-entry">
+Wallace, Hilary, David Gowing, Clare Lawson, Emma Rothero, and Ian
+Strachan. 2023. <span>“An Exploration of Oceanic Wet Grasslands in the
+<span>Scottish</span> Coastal Lowlands.”</span> <em>British
+Wildlife</em>, December. <a href="https://www.britishwildlife.com/article/article-volume-35-number-3-page-193-200/">https://www.britishwildlife.com/article/article-volume-35-number-3-page-193-200/</a>.
+</div>
 <div id="ref-wallace2018" class="csl-entry">
 Wallace, Hillary, and Laurence Jones. 2018. <span>“Monitoring of Forest
 Removal and Groundworks to Rejuvenate Dunes at Newborough Warren - Ynys

diff --git a/JOSS/paper.md b/JOSS/paper.md
@@ -20,7 +20,7 @@ affiliations:
     index: 1
   - name: UK Centre for Ecology \& Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, United Kingdom
     index: 2
-date: "2024-04-13"
+date: "2024-04-15"
 bibliography: paper.bib
 output:
   html_document:
@@ -120,7 +120,7 @@ charophyte (*Charophyta*) taxa, along with one unspecified 'algae' taxon present
 in the NVC floristic tables.
 The NVC communities present in `RMAVIS` are composed from @rodwell1991, 
 @rodwell1992, @rodwell1992a, @rodwell1995, @rodwell2000, 
-@wallace2017, and @prosser2023.
+@wallace2017, @prosser2023, and @wallace2023.
 Data for habitat correspondences is derived from: 
 the Joint Nature Conservation Committee (JNCC) Spreadsheet of Habitat 
 Correspondences [@jncc2008],

diff --git a/NEWS.md b/NEWS.md
@@ -3,14 +3,22 @@ title: "Release notes for `RMAVIS`"
 output: html_document
 ---
 
-# RMAVIS 1.000 (2024-04-XX)
+# RMAVIS 0.999 (2024-04-16)
 *   Modifications:
-      -   A
+      -   Updating to taxonomic backbone to use BSBI February 2024 taxon list.
+      -   Minimising the number of bundled datasets.
+      -   Removing assignNVC dependency.
 *   Fixes:
-      -   
+      -   Ensuring cover values are passed to surveyData_mat for use in Simpson 
+          diversity indices.
+      -   Ensure all assignment results reset upon Run Analysis, even if not run.
 *   New Features:
       -   Adding option to disable the calculation of similarities for quadrats.
       -   Adding Scottish oceanic wet grassland communities.
+      -   Ensuring all functions are covered by tests.
+      -   Adding JOSS paper.
+      -   Adding ability to turn quadrat similarities on or off.
+      -   Adding Scottish oceanic wet grassland communities.
 
 # RMAVIS 0.995 (2024-04-01)
 *   Modifications:

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-1.0-green.svg)]()
+[![Generic badge](https://img.shields.io/badge/Version-0.999-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
@@ -3,7 +3,8 @@
 
 <!-- badges: start -->
 
-[![Generic badge](https://img.shields.io/badge/Version-1.0-green.svg)]()
+[![Generic
+badge](https://img.shields.io/badge/Version-0.999-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/data/acceptedSpecies.rda b/data/acceptedSpecies.rda
diff --git a/data/concordance.rda b/data/concordance.rda
diff --git a/data/master_data.rda b/data/master_data.rda
diff --git a/data/nvc_floristic_tables.rda b/data/nvc_floristic_tables.rda
diff --git a/data/nvc_floristic_tables_numeric.rda b/data/nvc_floristic_tables_numeric.rda
diff --git a/data/nvc_pquad_dca.rda b/data/nvc_pquad_dca.rda
diff --git a/data/nvc_pquad_dca_centroids.rda b/data/nvc_pquad_dca_centroids.rda
diff --git a/data/nvc_pquad_dca_hulls.rda b/data/nvc_pquad_dca_hulls.rda
diff --git a/data/nvc_pquad_dca_noBryophytes.rda b/data/nvc_pquad_dca_noBryophytes.rda
diff --git a/data/nvc_pquad_dca_noBryophytes_centroids.rda b/data/nvc_pquad_dca_noBryophytes_centroids.rda
diff --git a/data/nvc_pquad_dca_noBryophytes_hulls.rda b/data/nvc_pquad_dca_noBryophytes_hulls.rda
diff --git a/data/nvc_pquads.rda b/data/nvc_pquads.rda
diff --git a/data/nvc_pquads_mean_unweighted_eivs.rda b/data/nvc_pquads_mean_unweighted_eivs.rda
diff --git a/data/nvc_pquads_mean_unweighted_eivs_noBryophytes.rda b/data/nvc_pquads_mean_unweighted_eivs_noBryophytes.rda
diff --git a/data/nvc_pquads_wide.rda b/data/nvc_pquads_wide.rda
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -4,7 +4,7 @@ services:
     build:
       context: .
       dockerfile: Dockerfile
-    image: "<container registry url>/rmavis:v0.995"
+    image: "<container registry url>/rmavis:v1.0"
     container_name: "rmavis"
     restart: always
     privileged: true

diff --git a/docs/documentation.Rmd b/docs/documentation.Rmd
@@ -1,6 +1,6 @@
 ---
 title: "RMAVIS - Documentation"
-subtitle: "v1.0"
+subtitle: "v0.999"
 # output:
 #   bookdown::word_document2:
 # always_allow_html: true

diff --git a/docs/references.bib b/docs/references.bib
@@ -917,7 +917,8 @@ @article{wallace2023
   author  = {Wallace, Hilary and Gowing, David and Lawson, Clare and Rothero, Emma and Strachan, Ian},
   year    = {2023},
   month   = dec,
-  journal = {British Wildlife}
+  journal = {British Wildlife},
+  url = {https://www.britishwildlife.com/article/article-volume-35-number-3-page-193-200/}
 }
 
 @article{wang2021a,

diff --git a/inst/extdata/acceptedSpecies.rds b/inst/extdata/acceptedSpecies.rds
diff --git a/inst/extdata/concordance.rds b/inst/extdata/concordance.rds
diff --git a/inst/extdata/master_data.rds b/inst/extdata/master_data.rds