First commit for v1.1 changes

NEWS.md

@@ -1,3 +1,33 @@
+# RMAVIS 1.1.0 ()
+*   Modifications:
+      -   Changing the minimum number of plots per group for Czekanowski similarity
+          calculations to 2.
+      -   Tidying the names and order of the RMAVIS results .xlsx download.
+      -   Changing "National Reference Spaces" option in the MVA module to
+          "Reference Spaces" and altering the module so that the local reference
+          ordinations are also linked to this option.
+      -   Updating the taxonomic backbone to the XXXXXX UKSI release ().
+      -   Updating the habitat correspondences to include a more comprehensive
+          set of NVC-to-EUNIS correspondences, floodplain meadows correspondences,
+          gap-filled NPMS habitat correspondences, and .......
+*   Fixes: NA
+*   New Features:
+      -   Adding the ability to trim leading and trailing white space from data
+          in the survey data validation module.
+      -   Adding the ability to lump taxa into higher ranks,
+          where the parent taxa of a higher rank exist in the NVC floristic tables,
+          but the lower rank taxa do not.
+          This ensures that related taxon concepts are matched, where desired.
+          For example, using this functionality one could lump 
+          Festuca rubra s.s. into Festuca rubra agg.
+      -   Adding additional NVC community attributes to the NVC lookup table,
+          floristic tables, and ... modules.
+      -   Adding an option to view the min, mean, and max cover values to
+          composed floristic tables.
+      -   Adding a new application section "NicheModels", where ecological
+          niche models can be viewed and used to estimate the probability of
+          occurrence.
+
 # RMAVIS 1.0.1 (2024-08-08)
 *   Modifications: NA
 *   Fixes:

README.md

@@ -4,7 +4,7 @@
 <!-- badges: start -->
 
 [![Generic
-badge](https://img.shields.io/badge/Version-1.0.1-green.svg)]()
+badge](https://img.shields.io/badge/Version-1.1.0-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)
@@ -27,12 +27,15 @@ conservation community.
 
 ## Structure
 
-There are 5 main sections in `RMAVIS` at present.
+There are 7 main sections in `RMAVIS` at present.
 
 **Home** - Provides outlining information.
 
-**Application** - The core of `RMAVIS`, containing the actual
-application.
+**Core** - The core of the `RMAVIS` application, containing the functionality
+present in the original v1.0 release.
+
+**NicheModels** - Contains the ability to view the ecological niche models for
+selected plant species and make occurrence probability predictions.
 
 **NVC Lookup** - Contains a searchable table, which can be used to
 retrieve the full name of an NVC community using an NVC community or
@@ -66,13 +69,17 @@ app, these are also made available through the `RMAVIS` package.
 
 ## Reccomended Citation
 
-To reference `RMAVIS` please cite the JOSS paper as follows:
+To reference the core `RMAVIS` application please cite the JOSS paper as follows:
 
 Marshall et al., (2024). RMAVIS v1.0: a Shiny application for the
 analysis of vegetation survey data and assignment to GB NVC communities.
 Journal of Open Source Software, 9(100), 6682,
 <https://doi.org/10.21105/joss.06682>
 
+To reference the ecological niche models please cite the..............
+
+To cite a specific version of RMAVIS.................
+
 ## Feedback
 
 To report a bug please submit a Github issue
@@ -82,10 +89,12 @@ form [here](https://forms.office.com/e/ByLgRPjT8J), or send an email to
 
 ## Acknowledgements
 
-The development of this app was partly supported by the UK‐SCAPE
-programme delivering National Capability (NE/R016429/1) funded by the
+The development of v1.0 of the app was partly supported by the UK‐SCAPE
+program delivering National Capability (NE/R016429/1) funded by the
 Natural Environment Research Council.
 
+The development of v1.1 of the app was supported by................
+
 We would like to thank Lindsay Maskell, Lucy Ridding, Barry Jobson,
 Colin Conroy, Andy McMullen, John Handley, Michael Tso, Simon Rolph,
 Cristina Martin Hernandez, and George Linney for testing RMAVIS.

inst/app/NEWS.md

@@ -1,3 +1,31 @@
+# RMAVIS 1.1.0 ()
+*   Modifications:
+      -   Changing the minimum number of plots per group for Czekanowski similarity
+          calculations to 2.
+      -   Tidying the names and order of the RMAVIS results .xlsx download.
+      -   Changing "National Reference Spaces" option in the MVA module to
+          "Reference Spaces" and altering the module so that the local reference
+          ordinations are also linked to this option.
+      -   Updating the taxonomic backbone to the XXXXXX UKSI release ().
+      -   Updating the habitat correspondences to include a more comprehensive
+          set of NVC-to-EUNIS correspondences, floodplain meadows correspondences,
+          gap-filled NPMS habitat correspondences, and .......
+*   Fixes: NA
+*   New Features:
+      -   Adding the ability to trim leading and trailing white space from data
+          in the survey data validation module.
+      -   Adding the ability to lump taxa into higher ranks,
+          where the parent taxa of a higher rank exist in the NVC floristic tables,
+          but the lower rank taxa do not.
+          This ensures that related taxon concepts are matched, where desired.
+          For example, using this functionality one could lump 
+          Festuca rubra s.s. into Festuca rubra agg.
+      -   Adding additional NVC community attributes to the NVC lookup table,
+          floristic tables, and ... modules.
+      -   Adding an option to view the min, mean, and max cover values to
+          composed floristic tables.
+      -   Adding a new application section "NicheModels" ....
+
 # RMAVIS 1.0.1 (2024-08-08)
 *   Modifications: NA
 *   Fixes:

inst/app/README.md

@@ -4,7 +4,7 @@
 <!-- badges: start -->
 
 [![Generic
-badge](https://img.shields.io/badge/Version-1.0.1-green.svg)]()
+badge](https://img.shields.io/badge/Version-1.1.0-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)
@@ -27,12 +27,15 @@ conservation community.
 
 ## Structure
 
-There are 5 main sections in `RMAVIS` at present.
+There are 7 main sections in `RMAVIS` at present.
 
 **Home** - Provides outlining information.
 
-**Application** - The core of `RMAVIS`, containing the actual
-application.
+**Core** - The core of the `RMAVIS` application, containing the functionality
+present in the original v1.0 release.
+
+**NicheModels** - Contains the ability to view the ecological niche models for
+selected plant species and make occurrence probability predictions.
 
 **NVC Lookup** - Contains a searchable table, which can be used to
 retrieve the full name of an NVC community using an NVC community or
@@ -66,13 +69,17 @@ app, these are also made available through the `RMAVIS` package.
 
 ## Reccomended Citation
 
-To reference `RMAVIS` please cite the JOSS paper as follows:
+To reference the core `RMAVIS` application please cite the JOSS paper as follows:
 
 Marshall et al., (2024). RMAVIS v1.0: a Shiny application for the
 analysis of vegetation survey data and assignment to GB NVC communities.
 Journal of Open Source Software, 9(100), 6682,
 <https://doi.org/10.21105/joss.06682>
 
+To reference the ecological niche models please cite the..............
+
+To cite a specific version of RMAVIS.................
+
 ## Feedback
 
 To report a bug please submit a Github issue
@@ -82,10 +89,12 @@ form [here](https://forms.office.com/e/ByLgRPjT8J), or send an email to
 
 ## Acknowledgements
 
-The development of this app was partly supported by the UK‐SCAPE
-programme delivering National Capability (NE/R016429/1) funded by the
+The development of v1.0 of the app was partly supported by the UK‐SCAPE
+program delivering National Capability (NE/R016429/1) funded by the
 Natural Environment Research Council.
 
+The development of v1.1 of the app was supported by................
+
 We would like to thank Lindsay Maskell, Lucy Ridding, Barry Jobson,
 Colin Conroy, Andy McMullen, John Handley, Michael Tso, Simon Rolph,
 Cristina Martin Hernandez, and George Linney for testing RMAVIS.

inst/app/docs/documentation.Rmd

@@ -304,7 +304,8 @@ $b$ represents the species present in one site but not the other (${X \cap Y}$),
 and the converse for $c$ (${X \cup Y}$).
 
 > Please note that Site and Group similarities will not be calculated
-> for Years and Year-Group combinations with less than 5 sample plots
+> for Years and Year-Group combinations with less than 2 sample plots.
+> It is highly reccomended that 5 or more plots are in each group.
 
 ### Pseudo-Quadrat Methodology
 

inst/app/modules/nvcAssignment_server.R

@@ -190,7 +190,7 @@ nvcAssignment <- function(input, output, session, setupData, surveyData, surveyD
       surveyDataSummary <- surveyDataSummary()
 
       # Retrieve the site and group ID's for which there are less than the threshold 
-      threshold <- 5
+      threshold <- 2
       site_group_ids_remove <- surveyDataSummary$surveyDataStructure$quadratsPerID |>
         dplyr::filter(n < threshold) |>
         dplyr::pull(ID)

inst/app/modules/sidebar_ui.R

@@ -1214,7 +1214,7 @@ sidebarUI <- function(id){
                 Select the RMAVIS outputs to include in the report.
                 
                 Please note that selecting the 'Survey Table' option may produce
-                a long report if a large quantity of data is submitted to
+                a *very* long report if a large quantity of data is submitted to
                 RMAVIS.
                 "
               ),

inst/app/modules/ui.R

@@ -44,7 +44,7 @@ ui <- bslib::page_navbar(
 
   bslib::nav_panel(
 
-    "Application",
+    "Core",
 
     bslib::layout_sidebar(
 
@@ -180,6 +180,34 @@ ui <- bslib::page_navbar(
 
   ),
 
+  bslib::nav_panel(
+
+    "NicheModels",
+
+    bslib::layout_sidebar(
+
+      sidebar = sidebarUI(id = "sidebar_id_nm"),
+
+      bslib::navset_card_tab(
+
+        bslib::nav_panel(
+
+          full_screen = TRUE,
+
+          bslib::card_header("Data Input"),
+
+          value = "nmDataInput_panel"#,
+
+          # surveyDataUI(id = "surveyData_id_1")
+
+        )
+
+      )
+
+    ),
+
+  ),
+
   bslib::nav_panel(
 
     "NVC Lookup",