Merge branch 'develop'

ZekeMarshall · ZekeMarshall · commit 32074dcae231 · 2025-07-29T10:27:37.000+01:00
diff --git a/CITATION.cff b/CITATION.cff
@@ -3,7 +3,7 @@ message: If you use this software, please cite our article in the Journal of Ope
 doi: 10.5281/zenodo.10818640
 repository-code: 'https://github.com/NERC-CEH/RMAVIS'
 license: LGPL-3.0
-version: v1.1.2
+version: v1.1.3
 type: software
 authors:
   - given-names: Zeke
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: RMAVIS
 Title: Assign Vegetation Survey Data to GB NVC Communities
-Version: 1.1.2
+Version: 1.1.3
 Date: 2025-07-28
 Authors@R: c(person(given = "Zeke",
                     family = "Marshall",
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# RMAVIS 1.1.3 (29-07-2025)
+*   Modifications: NA
+*   Fixes:
+      -   Ensuring order of execution for NVC assignment is correct, i.e. floristic tables must be composed and not NULL before group similarity calculations.
+*   New Features: NA
+
 # RMAVIS 1.1.2 (28-07-2025)
 *   Modifications: NA
 *   Fixes:
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-1.1.2-green.svg)]()
+[![Generic badge](https://img.shields.io/badge/Version-1.1.3-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-1.1.2-green.svg)]()
+badge](https://img.shields.io/badge/Version-1.1.3-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/inst/app/NEWS.md b/inst/app/NEWS.md
@@ -1,3 +1,9 @@
+# RMAVIS 1.1.3 (29-07-2025)
+*   Modifications: NA
+*   Fixes:
+      -   Ensuring order of execution for NVC assignment is correct, i.e. floristic tables must be composed and not NULL before group similarity calculations.
+*   New Features: NA
+
 # RMAVIS 1.1.2 (28-07-2025)
 *   Modifications: NA
 *   Fixes:
diff --git a/inst/app/README.md b/inst/app/README.md
@@ -4,7 +4,7 @@
 <!-- badges: start -->
 
 [![Generic
-badge](https://img.shields.io/badge/Version-1.1.2-green.svg)]()
+badge](https://img.shields.io/badge/Version-1.1.3-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/inst/app/docs/documentation.Rmd b/inst/app/docs/documentation.Rmd
@@ -1,6 +1,6 @@
 ---
 title: "RMAVIS - Documentation"
-subtitle: "v1.1.2"
+subtitle: "v1.1.3"
 # output:
 #   bookdown::word_document2:
 # always_allow_html: true
diff --git a/inst/app/modules/data_entry/deSidebar_server.R b/inst/app/modules/data_entry/deSidebar_server.R
@@ -157,7 +157,7 @@ deSidebar <- function(input, output, session,
     filename = function() {
       
       paste0("RMAVIS.SurveyData.",
-             "v1-1-2.",
+             "v1-1-3.",
              format(Sys.time(), "%y-%m-%d.%H-%M-%S"),
              ".csv",
              sep="")
@@ -180,7 +180,7 @@ deSidebar <- function(input, output, session,
     filename = function() {
       
       paste0("RMAVIS.AcceptedTaxa.",
-             "v1-1-2",
+             "v1-1-3",
              ".csv",
              sep="")
       
@@ -199,7 +199,7 @@ deSidebar <- function(input, output, session,
     filename = function() {
       
       paste0("RMAVIS.TaxonomicBackbone.",
-             "v1-1-2",
+             "v1-1-3",
              ".csv",
              sep="")
       
@@ -218,7 +218,7 @@ deSidebar <- function(input, output, session,
     filename = function() {
       
       paste0("RMAVIS.TaxonLookup.",
-             "v1-1-2",
+             "v1-1-3",
              ".csv",
              sep="")
       
diff --git a/inst/app/modules/news_ui.R b/inst/app/modules/news_ui.R
@@ -14,7 +14,7 @@ newsUI <- function(id) {
         
         shiny::markdown(
         '
-        The latest versions of RMAVIS (v1.1.2, v1.1.1, and v1.1.0) contain a number of breaking changes relative to the v1.0.1 release.
+        The latest versions of RMAVIS (v1.1.3, v1.1.2, v1.1.1, and v1.1.0) contain a number of breaking changes relative to the v1.0.1 release.
         
         First, is a major update to the taxonomy, which is now aligned with version 20250703a of the UKSI, available <a href="https://data.nhm.ac.uk/dataset/uk-species-inventory-simplified-copy/" target="_blank">here</a>.
         A csv of the taxonomic backbone can also be downloaded from the Data Entry section of RMAVIS.
diff --git a/inst/app/modules/nvc_analysis/nvcAssignment_server.R b/inst/app/modules/nvc_analysis/nvcAssignment_server.R
@@ -30,6 +30,8 @@ nvcAssignment <- function(input, output, session, setupData, surveyData, surveyD
   
   observe({
     
+    shiny::req(!is.null(floristicTables()))
+    
     shiny::isolate({
       setupData <- setupData()
       floristicTables <- floristicTables()
@@ -39,7 +41,7 @@ nvcAssignment <- function(input, output, session, setupData, surveyData, surveyD
     comp_ft_rval(setupData$floristic_tables)
     
   }) |>
-    bindEvent(runAnalysis(),
+    bindEvent(floristicTables(),
               ignoreInit = FALSE,
               ignoreNULL = TRUE)
   
@@ -184,7 +186,8 @@ nvcAssignment <- function(input, output, session, setupData, surveyData, surveyD
   
   observe({
     
-    shiny::req(!is.null(floristicTables()))
+    shiny::req(!is.null(samp_ft_rval()))
+    shiny::req(!is.null(comp_ft_rval()))
     shiny::req(surveyDataSummary())
     
     shinybusy::show_modal_spinner(
diff --git a/inst/app/modules/nvc_analysis/report_server.R b/inst/app/modules/nvc_analysis/report_server.R
@@ -27,7 +27,7 @@ report <- function(input, output, session,
     
     filename = function() {
       paste0("RMAVIS.Report.",
-             "v1-1-2.",
+             "v1-1-3.",
              format(Sys.time(), "%y-%m-%d.%H-%M-%S"),
              ".pdf",
              sep="")
diff --git a/inst/app/modules/nvc_analysis/sidebar_server.R b/inst/app/modules/nvc_analysis/sidebar_server.R
@@ -568,7 +568,7 @@ sidebar <- function(input, output, session,
     filename = function() {
       
       paste0("RMAVIS.Results.",
-             "v1-1-2.",
+             "v1-1-3.",
              format(Sys.time(), "%y-%m-%d.%H-%M-%S"),
              ".xlsx",
              sep="")
diff --git a/inst/app/modules/nvc_information/nvcInfoSidebar_server.R b/inst/app/modules/nvc_information/nvcInfoSidebar_server.R
@@ -8,7 +8,7 @@ nvcInfoSidebar <- function(input, output, session, nvcCommNamesLookup, nvcFlorTa
     filename = function() {
       
       paste0("RMAVIS.NVC.Information.",
-             "v1-1-2",
+             "v1-1-3",
              ".xlsx",
              sep="")
       
diff --git a/inst/app/report/Report.Rmd b/inst/app/report/Report.Rmd
@@ -147,7 +147,7 @@ reportOptions_options <- list(`NVC Assignment` = c("Site, Czekanowski" = "nvcAss
 
 ```{r RMAVISVersion, echo=FALSE, message=FALSE, warning=FALSE, results='asis'}
 
-cat("**Version:** ", as.character("v1.1.2"), sep = "")
+cat("**Version:** ", as.character("v1.1.3"), sep = "")
 
 ```
 
diff --git a/inst/app/www/documentation.html b/inst/app/www/documentation.html
@@ -1712,7 +1712,7 @@
 
 
 <h1 class="title toc-ignore">RMAVIS - Documentation</h1>
-<h3 class="subtitle">v1.1.2</h3>
+<h3 class="subtitle">v1.1.3</h3>
 
 </div>
 

Original file line number	Diff line number	Diff line change
`@@ -14,7 +14,7 @@ newsUI <- function(id) {`
`14`	`14`
`15`	`15`	`shiny::markdown(`
`16`	`16`	`'`
`17`		`- The latest versions of RMAVIS (v1.1.2, v1.1.1, and v1.1.0) contain a number of breaking changes relative to the v1.0.1 release.`
	`17`	`+ The latest versions of RMAVIS (v1.1.3, v1.1.2, v1.1.1, and v1.1.0) contain a number of breaking changes relative to the v1.0.1 release.`
`18`	`18`
`19`	`19`	`First, is a major update to the taxonomy, which is now aligned with version 20250703a of the UKSI, available <a href="https://data.nhm.ac.uk/dataset/uk-species-inventory-simplified-copy/" target="_blank">here</a>.`
`20`	`20`	`A csv of the taxonomic backbone can also be downloaded from the Data Entry section of RMAVIS.`