Merge branch 'main' into develop

ZekeMarshall · ZekeMarshall · commit e0688106b46b · 2025-07-28T13:01:44.000+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: v1.1.1
+version: v1.1.2
 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: 1.1.1
+Version: 1.1.2
 Date: 2025-07-28
 Authors@R: c(person(given = "Zeke",
                     family = "Marshall",
@@ -53,9 +53,10 @@ Imports:
   stringr,
   tibble,
   tidyr,
-  UKVegTB,
   vegan,
   writexl
+Remotes:
+   github::NERC-CEH/UKVegTB@v0.1.2
 Suggests:
   testthat,
   tinytex
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# RMAVIS 1.1.2 (28-07-2025)
+*   Modifications: NA
+*   Fixes:
+      -   Adding UKVegTB v0.1.2 as a remote dependency in the Description file.
+*   New Features: NA
+
 # RMAVIS 1.1.1 (28-07-2025)
 *   Modifications:
       -   Adding argument 'factor_constancy' to `RMAVIS::composeSyntopicTables` which controls whether the constancy column is returned as a factor or not.
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-1.1.1-green.svg)]()
+[![Generic badge](https://img.shields.io/badge/Version-1.1.2-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-1.1.1-green.svg)]()
+badge](https://img.shields.io/badge/Version-1.1.2-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/deploy.R b/deploy.R
@@ -12,4 +12,4 @@ rsconnect::deployApp(appDir = "./inst/app",
                      # appName = "rmavis", 
                      # appTitle = "RMAVIS",
                      appId = 321,
-                     forceUpdate = TRUE)
+                     forceUpdate = TRUE)
diff --git a/inst/app/NEWS.md b/inst/app/NEWS.md
@@ -1,3 +1,9 @@
+# RMAVIS 1.1.2 (28-07-2025)
+*   Modifications: NA
+*   Fixes:
+      -   Adding UKVegTB v0.1.2 as a remote dependency in the Description file.
+*   New Features: NA
+
 # RMAVIS 1.1.1 (28-07-2025)
 *   Modifications:
       -   Adding argument 'factor_constancy' to `RMAVIS::composeSyntopicTables` which controls whether the constancy column is returned as a factor or not.
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-1.1.1-green.svg)]()
+badge](https://img.shields.io/badge/Version-1.1.2-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: "v1.1.1"
+subtitle: "v1.1.2"
 # 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.",
-             "v1-1-1.",
+             "v1-1-2.",
              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.",
-             "v1-1-1",
+             "v1-1-2",
              ".csv",
              sep="")
       
@@ -199,7 +199,7 @@ deSidebar <- function(input, output, session,
     filename = function() {
       
       paste0("RMAVIS.TaxonomicBackbone.",
-             "v1-1-1",
+             "v1-1-2",
              ".csv",
              sep="")
       
@@ -218,7 +218,7 @@ deSidebar <- function(input, output, session,
     filename = function() {
       
       paste0("RMAVIS.TaxonLookup.",
-             "v1-1-1",
+             "v1-1-2",
              ".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 (v1.1.1 and v1.1.0) contain a number of breaking changes relative to the v1.0.1 release.
+        The latest versions of RMAVIS (v1.1.2, 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.
@@ -40,7 +40,7 @@ newsUI <- function(id) {
         or
         <a href="https://zenodo.org/search?q=parent.id%3A10818640&f=allversions%3Atrue&l=list&p=1&s=10&sort=version" target="_blank">Zenodo</a>.
         
-        Special thanks again to Colin Conroy and Barry Jobson for testing v1.1.1 and v1.1.0 of RMAVIS!
+        Special thanks again to Colin Conroy and Barry Jobson for testing v1.1.2, v1.1.1, and v1.1.0 of RMAVIS!
         '
         )
         
@@ -64,4 +64,4 @@ newsUI <- function(id) {
     )
   )
   
-}
+}
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.",
-             "v1-1-1.",
+             "v1-1-2.",
              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.",
-             "v1-1-1.",
+             "v1-1-2.",
              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.",
-             "v1-1-1",
+             "v1-1-2",
              ".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("v1.1.1"), sep = "")
+cat("**Version:** ", as.character("v1.1.2"), 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">v1.1.1</h3>
+<h3 class="subtitle">v1.1.2</h3>
 
 </div>
 
