Version 0.9993

NERC-CEH · Apr 21, 2024 · 88e5847 · 88e5847
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diff --git a/CITATION.cff b/CITATION.cff
@@ -34,4 +34,4 @@ keywords:
   - NVC
   - Vegetation Science
   - Vegetation Survey
-license: MIT
+license: CC BY 4.0
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: RMAVIS
 Title: Assign Vegetation Survey Data to GB NVC Communities
-Version: 0.9992
-Date: 2024-04-17
+Version: 0.9993
+Date: 2024-04-21
 Authors@R: c(person(given = "Zeke",
                     family = "Marshall",
                     role = c("aut", "cre"),

diff --git a/NEWS.md b/NEWS.md
@@ -3,6 +3,13 @@ title: "Release notes for `RMAVIS`"
 output: html_document
 ---
 
+# RMAVIS 0.9993 (2024-04-21)
+*   Modifications:
+      -   Changing licence to CC BY 4.0 ready for v1.
+*   Fixes:
+      -   Fixing issue where group-re-allocation table fails if quadrat ID's are integers.
+*   New Features: NA
+
 # RMAVIS 0.9992 (2024-04-17)
 *   Modifications:
       -   Updating author list.

diff --git a/README.Rmd b/README.Rmd
@@ -14,10 +14,11 @@ knitr::opts_chunk$set(
 # RMAVIS
 
 <!-- badges: start -->
-[![Generic badge](https://img.shields.io/badge/Version-0.9992-green.svg)]()
+[![Generic badge](https://img.shields.io/badge/Version-0.9993-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)
+[![License: CC BY 4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)
 <!-- badges: end -->
 
 The RMAVIS R Shiny web application is a tool to assist in the assignment of vegetation plot

diff --git a/README.md b/README.md
@@ -4,12 +4,14 @@
 <!-- badges: start -->
 
 [![Generic
-badge](https://img.shields.io/badge/Version-0.9992-green.svg)]()
+badge](https://img.shields.io/badge/Version-0.9993-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)
+[![License: CC BY
+4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)
 <!-- badges: end -->
 
 The RMAVIS R Shiny web application is a tool to assist in the assignment

diff --git a/app.R b/app.R
@@ -35,7 +35,7 @@ library(writexl)
 library(vegan)
 
 # Render documentation ----------------------------------------------------
-rmarkdown::render(input = "docs/documentation.Rmd",  output_dir = "www")
+# rmarkdown::render(input = "docs/documentation.Rmd",  output_dir = "www")
 
 # Source sub-modules ------------------------------------------------------
 source("modules/privacy_ui.R", local = TRUE)

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -4,7 +4,7 @@ services:
     build:
       context: .
       dockerfile: Dockerfile
-    image: "<container registry url>/rmavis:v1.0"
+    image: "<container registry url>/rmavis:v0.9993"
     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: "v0.9992"
+subtitle: "v0.9993"
 # output:
 #   bookdown::word_document2:
 # always_allow_html: true
@@ -107,8 +107,8 @@ development of TABLEFIT [@hill1989; @marrs2019] and was followed by MATCH
 [@malloch1998].
 The most recent program, the Modular Analysis of Vegetation Information System 
 (MAVIS), was developed as a windows application in 2000 and was a DEFRA-funded
-output of the ECOFACT project [@bunce1999].
-The latest version released in 2016 [@smart2016mavis].
+output of the ECOFACT project [@bunce1999], with the latest version released in 
+2016 [@smart2016mavis].
 
 This R Shiny implementation of MAVIS (`RMAVIS`) is the newest program in this
 series, aiming to provide a web-based and easily operable system which
@@ -780,13 +780,17 @@ example dataset.
 
 # Recommended Citation
 
-To reference `RMAVIS` please cite the JOSS paper (in prep)
+To reference `RMAVIS` please cite the JOSS paper (in prep)...
 
 ```
 
 ```
 
-and the Zenodo repository for the particular version used, which can be found
-here https://zenodo.org/records/10903218.
+Alternatively, use either the Zenodo DOI for all versions as follows:
+
+Marshall, Z., Smart, S. M., Harrower, C., & Marrs, R. (2024). RMAVIS. Zenodo. 
+https://zenodo.org/doi/10.5281/zenodo.10818640
+
+or the DOI associated with a particular release.
 
 # References
diff --git a/modules/surveyDataValidator_server.R b/modules/surveyDataValidator_server.R
@@ -135,6 +135,7 @@ surveyDataValidator <- function(input, output, session, setupData, surveyData, s
 
     surveyData <- surveyData()
     surveyData_original <- surveyData$surveyData_original
+    assign(x = "surveyData_original", value = surveyData_original, envir = .GlobalEnv)
     surveyData_long <- surveyData$surveyData_long
     surveyData_wide <- surveyData$surveyData_wide
     surveyData_mat <- surveyData$surveyData_mat

diff --git a/modules/surveyData_server.R b/modules/surveyData_server.R
@@ -425,11 +425,13 @@ surveyData <- function(input, output, session, uploadDataTable, setupData, surve
 
     isolate({
 
-      surveyData <- rhandsontable::hot_to_r(input$surveyData)
+      surveyData <- rhandsontable::hot_to_r(input$surveyData) |>
+        dplyr::mutate("Quadrat" = as.character(Quadrat))
 
       if(!is.null(reallocateGroupsTable())){
 
-        reallocateGroupsTable <- reallocateGroupsTable()
+        reallocateGroupsTable <- reallocateGroupsTable() |>
+          dplyr::mutate("Quadrat" = as.character(Quadrat))
 
         surveyData_corrected <- surveyData |>
           tibble::as_tibble() |>

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("v0.9992"), sep = "")
+cat("**Version:** ", as.character("v0.9993"), sep = "")
 
 ```
 
@@ -373,7 +373,7 @@ if("habitatCorrespondenceSite" %in% reportOptions){
   
   kableExtra::kbl(x = habCor_prepped, format = "latex", booktabs = TRUE,
                   longtable = TRUE, linesep = "",
-                  caption = "The habitats associated with the top-N fitting NVC communities according to other") |>
+                  caption = "The habitats associated with the top-N fitting NVC communities from alternative habitat classifications.") |>
     kableExtra::kable_styling(font_size = 7) |>
     kableExtra::kable_styling(latex_options = c("repeat_header", "HOLD_position")) |>
     kableExtra::landscape()

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">v0.9992</h3>
+<h3 class="subtitle">v0.9993</h3>
 
 </div>
 
@@ -1761,8 +1761,8 @@ <h1><span class="header-section-number">1</span> Introduction</h1>
 <span class="citation">(<a href="#ref-malloch1998">Malloch 1998</a>)</span>.
 The most recent program, the Modular Analysis of Vegetation Information System
 (MAVIS), was developed as a windows application in 2000 and was a DEFRA-funded
-output of the ECOFACT project <span class="citation">(<a href="#ref-bunce1999">Bunce et al. 1999</a>)</span>.
-The latest version released in 2016 <span class="citation">(<a href="#ref-smart2016mavis">Smart, Goodwin, and Wallace 2016</a>)</span>.</p>
+output of the ECOFACT project <span class="citation">(<a href="#ref-bunce1999">Bunce et al. 1999</a>)</span>, with the latest version released in
+2016 <span class="citation">(<a href="#ref-smart2016mavis">Smart, Goodwin, and Wallace 2016</a>)</span>.</p>
 <p>This R Shiny implementation of MAVIS (<code>RMAVIS</code>) is the newest program in this
 series, aiming to provide a web-based and easily operable system which
 can be updated and improved over time in response to user needs.</p>
@@ -2565,10 +2565,12 @@ <h1><span class="header-section-number">3</span> Acknowledgements</h1>
 </div>
 <div id="recommended-citation" class="section level1" number="4">
 <h1><span class="header-section-number">4</span> Recommended Citation</h1>
-<p>To reference <code>RMAVIS</code> please cite the JOSS paper (in prep)</p>
+<p>To reference <code>RMAVIS</code> please cite the JOSS paper (in prep)…</p>
 <pre><code></code></pre>
-<p>and the Zenodo repository for the particular version used, which can be found
-here <a href="https://zenodo.org/records/10903218" class="uri">https://zenodo.org/records/10903218</a>.</p>
+<p>Alternatively, use either the Zenodo DOI for all versions as follows:</p>
+<p>Marshall, Z., Smart, S. M., Harrower, C., &amp; Marrs, R. (2024). RMAVIS. Zenodo.
+<a href="https://zenodo.org/doi/10.5281/zenodo.10818640" class="uri">https://zenodo.org/doi/10.5281/zenodo.10818640</a></p>
+<p>or the DOI associated with a particular release.</p>
 </div>
 <div id="references" class="section level1 unnumbered">
 <h1>References</h1>