Merge branch 'v0.97'

R/create_constants.R

@@ -111,7 +111,7 @@ resultsViewNVCAssign_options <- c(#"Site, Jaccard" = "nvcAssignSiteJaccard",
                                   #"Group, Jaccard" = "nvcAssignGroupJaccard",
                                   "Site, Czekanowski" = "nvcAssignSiteCzekanowski",
                                   "Group, Czekanowski" = "nvcAssignGroupCzekanowski",
-                                  "Quadrat, Jaccard" = "nvcAssignQuadratJaccard"#,
+                                  "Quadrat, Jaccard" = "nvcAssignPlotJaccard"#,
                                   # "Quadrat, Czekanowski" = "nvcAssignQuadratCzekanowski"
                                   )
 
@@ -227,6 +227,6 @@ reportOptions_options <- list(#`NVC Assignment Pseudo-quadrat` = c("Site" = "nvc
                               `MVA` = c("National" = "mvaNationalReference",
                                         "Local (restricted)" = "mvaLocalReferenceRestricted",
                                         "Local (unrestricted)" = "mvaLocalReferenceUnrestricted"),
-                              `Survey Table` = c("Survey Table" = "surveyTable")
+                              `Survey Table` = c("Survey Table" = "surveyData")
     )
 

R/functions.R

@@ -1,19 +1,19 @@
 # Base R or tidyverse?
 
-# Convert surveyTable to surveyTableWide
+# Convert surveyData to surveyDataWide
 
-# Calculate DCA using surveyTableWide and selected nvc_pquad_dca_list DCA results
+# Calculate DCA using surveyDataWide and selected nvc_pquad_dca_list DCA results
 
 # Produce a DCA plot ggplot2 graph with points only
 
 # Produce a DCA plot ggplot2 graph with points and convex hulls
 
 # Produce a DCA plot ggplot2 graph with sample quadrat points and convex hulls
 
-# Calculate diversity metrics using surveyTable 
+# Calculate diversity metrics using surveyData 
 
-# Calculate mean cover-weighted EIVs using surveyTable
+# Calculate mean cover-weighted EIVs using surveyData
 
-# Calculate mean EIVs using surveyTable
+# Calculate mean EIVs using surveyData
 
 

R/load_packages.R

@@ -8,6 +8,7 @@ library(shinyjs)
 library(shinybusy)
 
 # General
+library(R6)
 library(rmarkdown)
 library(bookdown)
 library(tidyverse)

R/similarity_functions.R

@@ -25,15 +25,6 @@ similarityCzekanowski <- function(samp_df, comp_df,
                                   samp_weight_name, comp_weight_name,
                                   downweight_threshold = 0.2, downweight_value = 0.1){
 
-  assign(x = "samp_df", value = samp_df, envir = .GlobalEnv)
-  assign(x = "comp_df", value = comp_df, envir = .GlobalEnv)
-  assign(x = "samp_species_col", value = samp_species_col, envir = .GlobalEnv)
-  assign(x = "comp_species_col", value = comp_species_col, envir = .GlobalEnv)
-  assign(x = "samp_group_name", value = samp_group_name, envir = .GlobalEnv)
-  assign(x = "comp_group_name", value = comp_group_name, envir = .GlobalEnv)
-  assign(x = "samp_weight_name", value = samp_weight_name, envir = .GlobalEnv)
-  assign(x = "comp_weight_name", value = comp_weight_name, envir = .GlobalEnv)
-
   # Check argument types are correct
   checkmate::assertDataFrame(samp_df)
   checkmate::assertDataFrame(comp_df)

R/syntopicTable_functions.R

@@ -1,7 +1,7 @@
-# Compose floristic tables from surveyTable
-composeSyntopicTables <- function(surveyTable, group_cols, species_col_name = "Species", plot_col_name = "Quadrat"){
+# Compose floristic tables from surveyData
+composeSyntopicTables <- function(surveyData, group_cols, species_col_name = "Species", plot_col_name = "Quadrat"){
 
-  syntopicTables <- surveyTable |>
+  syntopicTables <- surveyData |>
     tidyr::unite(col = "ID", group_cols, sep = " - ", remove = TRUE) |>
     dplyr::select(ID, plot_col_name, species_col_name) |>
     dplyr::mutate("Present" = 1) |>

README.Rmd

@@ -14,27 +14,28 @@ knitr::opts_chunk$set(
 # RMAVIS
 
 <!-- badges: start -->
-[![Generic badge](https://img.shields.io/badge/Version-0.96-green.svg)]()
+[![Generic badge](https://img.shields.io/badge/Version-0.97-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)
 <!-- badges: end -->
 
 The RMAVIS R shiny web application is a tool to assist in the assignment of vegetation plot
-sample data to UK National Vegetation Classification units, with additional exploratory analysis.
+sample data to UK National Vegetation Classification units, with additional exploratory analyses.
 
 ## Running the app
 
 You can run RMAVIS from [GitHub](https://github.com/ZekeMarshall/RMAVIS) by cloning the 
 repository, calling `renv::restore()`, and then calling `shiny::runApp("app.R")`.
 
-If `renv::restore()` fails run `install.packages(unique(renv::dependencies()$Package), dependencies = TRUE)`. 
+If `renv::restore()` fails run `install.packages(unique(renv::dependencies()$Package), dependencies = TRUE)`.
+Note that whilst the correct dependencies will be installed, the versions may not match those in the renv.lock file.
 
 Future developments may support the release of RMAVIS as an R package.
 
 ## Hosting
 
 ### Posit Connect
 
-RMAVIS is currently hosted on the UKCEH Posit Connect server:
+RMAVIS is currently hosted on the UKCEH Posit Connect server: https://connect-apps.ceh.ac.uk/RMAVIS/
 
 ### Docker
 

README.md

@@ -4,15 +4,15 @@
 <!-- badges: start -->
 
 [![Generic
-badge](https://img.shields.io/badge/Version-0.96-green.svg)]()
+badge](https://img.shields.io/badge/Version-0.97-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)
 <!-- badges: end -->
 
 The RMAVIS R shiny web application is a tool to assist in the assignment
 of vegetation plot sample data to UK National Vegetation Classification
-units, with additional exploratory analysis.
+units, with additional exploratory analyses.
 
 ## Running the app
 
@@ -22,6 +22,8 @@ by cloning the repository, calling `renv::restore()`, and then calling
 
 If `renv::restore()` fails run
 `install.packages(unique(renv::dependencies()$Package), dependencies = TRUE)`.
+Note that whilst the correct dependencies will be installed, the
+versions may not match those in the renv.lock file.
 
 Future developments may support the release of RMAVIS as an R package.
 
@@ -30,6 +32,7 @@ Future developments may support the release of RMAVIS as an R package.
 ### Posit Connect
 
 RMAVIS is currently hosted on the UKCEH Posit Connect server:
+<https://connect-apps.ceh.ac.uk/RMAVIS/>
 
 ### Docker
 

app.R

@@ -11,7 +11,8 @@ source("R/load_data.R", local = TRUE)
 source("R/create_constants.R", local = TRUE)
 
 # Render documentation ----------------------------------------------------
-source("R/render_docs.R", local = TRUE) # This can be disabled if one wishes to pre-render the documentation manually.
+# This can be disabled if one wishes to pre-render the documentation manually.
+source("R/render_docs.R", local = TRUE)
 
 # Source functions --------------------------------------------------------
 source("R/syntopicTable_functions.R", local = TRUE)
@@ -34,17 +35,17 @@ source("modules/setupData_server.R", local = TRUE)
 source("modules/uploadData_ui.R", local = TRUE)
 source("modules/uploadData_server.R", local = TRUE)
 
-source("modules/surveyTable_ui.R", local = TRUE)
-source("modules/surveyTable_server.R", local = TRUE)
+source("modules/surveyData_ui.R", local = TRUE)
+source("modules/surveyData_server.R", local = TRUE)
 
-source("modules/surveyTableValidator_ui.R", local = TRUE)
-source("modules/surveyTableValidator_server.R", local = TRUE)
+source("modules/surveyDataValidator_ui.R", local = TRUE)
+source("modules/surveyDataValidator_server.R", local = TRUE)
 
-source("modules/surveyTableSummary_ui.R", local = TRUE)
-source("modules/surveyTableSummary_server.R", local = TRUE)
+source("modules/surveyDataSummary_ui.R", local = TRUE)
+source("modules/surveyDataSummary_server.R", local = TRUE)
 
-source("modules/surveyTableWide_ui.R", local = TRUE)
-source("modules/surveyTableWide_server.R", local = TRUE)
+source("modules/floristicTables_ui.R", local = TRUE)
+source("modules/floristicTables_server.R", local = TRUE)
 
 # source("modules/selectedPquads_server.R", local = TRUE)
 
@@ -54,9 +55,6 @@ source("modules/nvcAssignment_server.R", local = TRUE)
 source("modules/habCor_ui.R", local = TRUE)
 source("modules/habCor_server.R", local = TRUE)
 
-source("modules/floristicTables_ui.R", local = TRUE)
-source("modules/floristicTables_server.R", local = TRUE)
-
 source("modules/speciesFreq_ui.R", local = TRUE)
 source("modules/speciesFreq_server.R", local = TRUE)
 

docker-compose.yml

@@ -4,7 +4,7 @@ services:
     build:
       context: .
       dockerfile: Dockerfile
-    image: "<container registry url>/rmavis:v0.96"
+    image: "<container registry url>/rmavis:v0.97"
     container_name: "rmavis"
     restart: always
     privileged: true

docs/documentation.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "RMAVIS - Documentation"
-subtitle: "v0.96"
+subtitle: "v0.97"
 # output: 
 #   bookdown::word_document2:
 # always_allow_html: true
@@ -81,7 +81,7 @@ reportOptions_options <- list(`NVC Assignment` = c("Site, Czekanowski" = "nvcAss
                               `MVA` = c("National" = "mvaNationalReference",
                                         "Local (restricted)" = "mvaLocalReferenceRestricted",
                                         "Local (unrestricted)" = "mvaLocalReferenceUnrestricted"),
-                              `Survey Table` = c("Survey Table" = "surveyTable")
+                              `Survey Table` = c("Survey Table" = "surveyData")
     )
 
 ```
@@ -530,6 +530,16 @@ to be displayed in the MVA plots:
 Here the user may select any NVC community to display in the **National
 Reference** MVA plot only.
 
+**Group Survey Plots**
+
+Three options are available to 'group' the survey quadrat/plot data:
+
+-   No, the individual plots are left ungrouped.
+-   Group, mean DCA axis scores are calculated from the individual plots 
+    by group.
+-   Year, mean DCA axis scores are calculated from the individual plots
+    by year.
+
 **Survey Quadrat Selection**
 
 Three methods are available for subsetting the survey quadrats being
@@ -566,6 +576,7 @@ plots.
 -   Survey Quadrats, the survey quadrats entered in **Survey Data**.
 -   Pseudo-Quadrats, all pseudo-quadrats used in the DCA ordination.
 -   Reference Space, the convex hulls formed around the pseudo-quadrats.
+-   Reference Centroids, the centroids formed from the pseudo-quadrat DCA scores.
 -   Species, the species DCA axis scores.
 -   Unique Survey Species, the species present in the survey quadrats
     but absent in the top-fitted NVC communities pseudo-quadrats.
@@ -638,7 +649,7 @@ Marshall, Z., Smart, S., and Harrower, C.. (2024). RMAVIS.
 @misc{marshall2024,
   author = {Marshall, Z. and Smart, S. and Harrower, C.},
   title = {RMAVIS},
-  howpublished = {Available at https://connect-apps.ceh.ac.uk/RMAVIS/, version 0.96},
+  howpublished = {Available at https://connect-apps.ceh.ac.uk/RMAVIS/, version 0.97},
   month = {02},
   year  = {2024},
   note = {A R Shiny application for the assignment of vegetation survey data to National Vegetation Classification (NVC) communities, with additional exploratory analyses.}
@@ -649,6 +660,20 @@ Marshall, Z., Smart, S., and Harrower, C.. (2024). RMAVIS.
 
 <details>
 
+<summary>v0.97</summary>
+
+<strong>2024/03/XX</strong>
+
+-   Modifications: NA
+-   Fixes:
+      -   Updating documentation to reflect new MVA functionality.
+      -   Fixing group survey plots option in MVA module.
+-   New Features: NA
+
+</details>
+
+<details>
+
 <summary>v0.96</summary>
 
 <strong>2024/03/02</strong>
@@ -678,7 +703,7 @@ Marshall, Z., Smart, S., and Harrower, C.. (2024). RMAVIS.
     -   Making survey data availability table searchable.
     -   Changing nomenclature for releve to plot.
 -   Fixes:
-    -   Ensuring report renders correctly using new surveyTableSummary
+    -   Ensuring report renders correctly using new surveyDataSummary
         object data.
 -   New Features: NA
 

docs/documentation.html

@@ -970,7 +970,7 @@ <h1><span class="header-section-number">5</span> Release Log</h1>
 </ul></li>
 <li>Fixes:
 <ul>
-<li>Ensuring report renders correctly using new surveyTableSummary object data.</li>
+<li>Ensuring report renders correctly using new surveyDataSummary object data.</li>
 </ul></li>
 <li>New Features: NA</li>
 </ul>

modules/calcAvgEIVs_server.R

@@ -1,4 +1,4 @@
-calcAvgEIVs <- function(input, output, session, surveyTable, sidebar_options) {
+calcAvgEIVs <- function(input, output, session, surveyData, sidebar_options) {
 
   ns <- session$ns
 
@@ -268,7 +268,7 @@ calcAvgEIVs <- function(input, output, session, surveyTable, sidebar_options) {
 
   observe({
 
-    shiny::req(surveyTable())
+    shiny::req(surveyData())
 
     shinybusy::show_modal_spinner(
       spin = "fading-circle",
@@ -279,13 +279,14 @@ calcAvgEIVs <- function(input, output, session, surveyTable, sidebar_options) {
     # Isolate reactive objects
     shiny::isolate({
 
-      surveyTable <- surveyTable()
+      surveyData <- surveyData()
+      surveyData_long <- surveyData$surveyData_long
 
 
 # Calculate Weighted Mean HE Values ---------------------------------------
 
       # By Quadrat
-      weightedMeanHEValuesQuadrat <- surveyTable |>
+      weightedMeanHEValuesQuadrat <- surveyData_long |>
         dplyr::rename("species" = "Species") |>
         dplyr::left_join(master_data, by = "species",
                          relationship = "many-to-many") |>
@@ -340,7 +341,7 @@ calcAvgEIVs <- function(input, output, session, surveyTable, sidebar_options) {
 # Calculate Unweighted Mean HE Values -------------------------------------
 
       # By Quadrat
-      unweightedMeanHEValuesQuadrat <- surveyTable |>
+      unweightedMeanHEValuesQuadrat <- surveyData_long |>
         dplyr::rename("species" = "Species") |>
         dplyr::left_join(master_data, by = "species",
                          relationship = "many-to-many") |>