Merge devel into main

.github/workflows/check-standard.yaml

@@ -39,6 +39,10 @@ jobs:
         with:
           extra-packages: any::rcmdcheck
           needs: check
+      - name: Fix temporary out-of-sync binary packages
+        run: |
+            install.packages("MatrixModels", repos = "https://cloud.r-project.org", type = "source")
+        shell: Rscript {0}
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -35,6 +35,10 @@ jobs:
             any::bookdown
             local::.
           needs: website
+      - name: Fix temporary out-of-sync binary packages
+        run: |
+          install.packages("MatrixModels", repos = "https://cloud.r-project.org", type = "source")
+        shell: Rscript {0}
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}

CHANGELOG.md

@@ -7,6 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased](https://github.com/openghg/openghg/compare/0.2.0...HEAD)
 
+### Fixed
+
+- Fixed `model_viewer` app to work with random effect models - [PR #317](https://github.com/4DModeller/fdmr/pull/317)
+- Updated `plot_map_leaflet` to feature the same selection of basemap tiles as `mapview` and fix features not appearing - [PR #310](https://github.com/4DModeller/fdmr/pull/310)
+
+### Added
+- Added ocean heat content mapping tutorial - [PR #318](https://github.com/4DModeller/fdmr/pull/318)
+
 ## [0.2.0] - 2023-12-19
 
 ### Fixed

R/plot_mapping.R

@@ -102,7 +102,8 @@ plot_map_leaflet <- function(polygon_data = NULL,
                              wrapping = FALSE) {
   m <- leaflet::leaflet()
   m <- leaflet::addTiles(m)
-  m <- leaflet::addProviderTiles(m, leaflet::providers$Openstreetmap, group = "Satellite")
+  m <- leaflet::addProviderTiles(m, leaflet::providers$Esri.WorldImagery, group = "Satellite")
+  m <- leaflet::addProviderTiles(m, leaflet::providers$OpenTopoMap, group = "Topography")
   m <- leafem::addMouseCoordinates(m, native.crs = TRUE)
 
   # Store a vector of layers we add to the map,
@@ -161,7 +162,7 @@ plot_map_leaflet <- function(polygon_data = NULL,
 
   m <- leaflet::addLayersControl(m,
     position = "topright",
-    baseGroups = c("OSM", "Satellite"),
+    baseGroups = c("OSM", "Satellite", "Topography"),
     overlayGroups = layers,
     options = leaflet::layersControlOptions(collapsed = FALSE)
   )

R/shiny_modelviewer.R

@@ -35,6 +35,11 @@ model_viewer_shiny <- function(model_output, mesh, measurement_data, data_distri
   default_colours <- rownames(brewer_palettes[brewer_palettes$cat == "seq", ])
 
   plot_choices <- c("Range", "Stdev", "AR(1)", "Boxplot", "Density", "DIC")
+  if (base::is.null(parsed_model_output[["fixed_mean"]])) {
+    map_choices <- c("Random effect fields")
+  } else {
+    map_choices <- c("Predicted mean fields", "Random effect fields")
+  }
 
   ui <- bslib::page_fluid(
     theme = bslib::bs_theme(bootswatch = "cosmo"),
@@ -56,7 +61,7 @@ model_viewer_shiny <- function(model_output, mesh, measurement_data, data_distri
         shiny::fluidRow(
           shiny::column(
             4,
-            shiny::selectInput(inputId = "map_plot_type", label = "Plot type", choices = c("Predicted mean fields", "Random effect fields"), selected = "Predicted mean fields"),
+            shiny::selectInput(inputId = "map_plot_type", label = "Plot type", choices = map_choices, selected = map_choices[1]),
             shiny::selectInput(inputId = "map_data_type", label = "Data type", choices = c("Poisson", "Gaussian"), selected = data_distribution),
           ),
           shiny::column(

_pkgdown.yml

@@ -45,6 +45,8 @@ navbar:
           href: articles/hydro.html
         - text: "Priors exploration"
           href: articles/priors.html
+        - text: "Ocean heat content mapping"
+          href: articles/ohc_tutorial.html
         - text: ---
         - text: "FAQ"
         - text: INLA Crash FAQ