Fix merge conflicts

CHANGELOG.md

@@ -19,6 +19,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- Allowed reversal of colour palette and added raster plot legend in map plotter - [PR #229](https://github.com/4DModeller/fdmr/pull/229)
+- Added markers option to mesh plotter - [PR #230](https://github.com/4DModeller/fdmr/pull/230)
+
 ### Removed
 
 ## [0.1.0] - 2023-10-17
@@ -31,7 +34,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Clearer documentation on types expected by the `mesh_builder` tool - [PR #101](https://github.com/4DModeller/fdmr/pull/101)
 - Checks on the data types being passed into the `mesh_builder` tool - [PR #101](https://github.com/4DModeller/fdmr/pull/101)
 - Ability to plot either polygon or point data on Leaflet map of `mesh_builder` tool - [PR #101](https://github.com/4DModeller/fdmr/pull/101)
-- The ability to plot model predictions on a `leaflet` map in the our [Interactive priors Shiny app](https://4dmodeller.github.io/fdmr/articles/priors_app.html) - [PR #147](https://github.com/4DModeller/fdmr/pull/147)
+- The ability to plot model predictions on a `leaflet` map in the our [Model builder Shiny app](https://4dmodeller.github.io/fdmr/articles/modelbuilder.html) - [PR #147](https://github.com/4DModeller/fdmr/pull/147)
 - A new Shiny app to parse and plot INLA model output, letting users easily view model parameters and predictions on a map - [PR #158](https://github.com/4DModeller/fdmr/pull/158)
 
 ### Fixed

DESCRIPTION

@@ -54,7 +54,8 @@ Imports:
  promises,
  fmesher,
  purrr,
- shinyjs
+ shinyjs,
+ bslib
 Suggests: 
  bookdown,
  knitr,

R/plot_mapping.R

@@ -11,6 +11,7 @@
 #' @param polygon_fill_colour Polygon fill colour
 #' @param polygon_line_colour Polygon surrounding line colour
 #' @param polygon_line_weight Polygon surrounding line weight
+#' @param reverse Reverse the colour palette if TRUE
 #'
 #' @return leaflet::leaflet
 #' @export
@@ -24,7 +25,8 @@ plot_map <- function(polygon_data = NULL,
  polygon_fill_colour = "#E4572E",
  polygon_line_colour = "grey",
  polygon_line_weight = 1,
- polygon_fill_opacity = 0.6) {
+ polygon_fill_opacity = 0.6,
+ reverse = FALSE) {
  if (is.null(polygon_data) && is.null(raster_data)) {
  stop("Polygon or raster data must be given.")
  }
@@ -39,7 +41,7 @@ plot_map <- function(polygon_data = NULL,
 
  if (!is.null(polygon_data)) {
  if (!is.null(domain)) {
- colours <- leaflet::colorNumeric(palette = palette, domain = domain, reverse = FALSE)
+ colours <- leaflet::colorNumeric(palette = palette, domain = domain, reverse = reverse)
  polygon_fill_colour <- ~ colours(domain)
  m <- leaflet::addLegend(m,
  pal = colours,
@@ -61,12 +63,20 @@ plot_map <- function(polygon_data = NULL,
  }
 
  if (!is.null(raster_data)) {
+ colours <- leaflet::colorNumeric(palette = palette, domain = raster::values(raster_data), na.color=rgb(0,0,0,0), reverse = reverse)
  m <- leaflet::addRasterImage(m,
  x = raster_data,
  opacity = 0.75,
  group = "Raster",
  layerId = "raster",
- colors = palette,
+ colors = colours,
+ )
+ m <- leaflet::addLegend(m,
+ pal = colours,
+ values = raster::values(raster_data),
+ opacity = 0.75,
+ title = legend_title,
+ na.label = ""
  )
  layers <- append(layers, "Raster")
  }

R/plot_mesh.R

@@ -5,10 +5,12 @@
 #' that can be converted to a data.frame with longitude and latitude columns
 #' @param longitude_column Longitude column in spatial_data
 #' @param latitude_column Latitude column in spatial_data name
+#' @param markers Markers to display on top of mesh. A named list with latitude, longitude and label names must be given.
+#' Expects longitude name to be longitude, latitude name to be latitude, label name to be label.
 #'
 #' @return leaflet::leaflet
 #' @export
-plot_mesh <- function(mesh, spatial_data = NULL, longitude_column = "LONG", latitude_column = "LAT") {
+plot_mesh <- function(mesh, spatial_data = NULL, longitude_column = "LONG", latitude_column = "LAT", markers = NULL) {
  expected_crs <- "+proj=longlat +datum=WGS84"
  crs_string <- fmesher::fm_proj4string(mesh)
 
@@ -24,7 +26,6 @@ plot_mesh <- function(mesh, spatial_data = NULL, longitude_column = "LONG", lati
 
  spatial_mesh <- fdmr::mesh_to_spatial(mesh = mesh, crs = expected_crs)
 
-
  plot_polygons <- FALSE
  plot_points <- FALSE
  if (!is.null(spatial_data)) {
@@ -68,6 +69,11 @@ plot_mesh <- function(mesh, spatial_data = NULL, longitude_column = "LONG", lati
  overlay_groups <- append(overlay_groups, "Spatial")
  }
 
+ if (!is.null(markers)) {
+ m <- leaflet::addMarkers(m, lng = markers$longitude, lat = markers$latitude, label = markers$label, group = "Markers")
+ overlay_groups <- append(overlay_groups, "Markers")
+ }
+
  m <- leaflet::addLayersControl(m,
  position = "topright",
  baseGroups = c("OSM"),

R/shiny_priors.R → R/shiny_modelbuilder.R

@@ -108,13 +108,13 @@ model_builder_shiny <- function(spatial_data,
  # structure we can remove this
  busy_spinner <- get_busy_spinner()
 
- range0_tooltip <- "range0 and Prange jointly specify the complexity priors for the spatial range parameter ρ, in the relation that P(ρ < range0 ) = Prange.
+ range0_tooltip <- "range0 and Prange jointly specify the complexity priors for the spatial range parameter ρ, in the relation that P(ρ < range0 ) = Prange. 
  The spatial range parameter ρ is defined as the distance at which the spatial correlation between two locations is approximately 0"
- Prange_tooltip <- "Large values of Prange lead to a greater prior belief on small values of ρ."
-
+ Prange_tooltip <- "Large values of Prange lead to a greater prior belief on small values of ρ." 
+ 
  sigma0_tooltip <- "sigma0 and Psigma jointly specify the complexity priors for the marginal standard deviation of the field σ, in the relation of P(σ > sigma0) = Psigma."
  Psigma_tooltip <- "Large values of Psigma lead to a greater prior belief on large values of σ."
-
+ 
  prior_alpha_tooltip <- "prior_alpha and pg_alpha jointly specify the complexity priors for the temporal autocorrelation parameter α, in the relation that P(α > prior_alpha) = pg_alpha."
  pg_alpha_tooltip <- "Large values of pg_alpha lead to a greater prior belief on large values of α"
 
@@ -214,6 +214,7 @@ model_builder_shiny <- function(spatial_data,
  ),
  shiny::tabPanel(
  "Features",
+ class = "p-3 border",
  shiny::fluidRow(
  shiny::column(
  6,
@@ -225,17 +226,23 @@ model_builder_shiny <- function(spatial_data,
  shiny::selectInput(inputId = "data_dist", label = "Data distribution", choices = c("Poisson", "Gaussian"), selected = data_distribution),
  )
  ),
- shiny::checkboxGroupInput(inputId = "features", label = "Features", choices = features),
- shiny::checkboxInput(inputId = "f_func", label = "Add f()", value = FALSE),
- shiny::actionButton(inputId = "clear", label = "Clear"),
  shiny::fluidRow(
- shiny::h2("Formula"),
- shiny::textOutput(outputId = "final_equation"),
- style = "height:20vh;"
+ shiny::column(
+ 6,
+ shiny::checkboxGroupInput(inputId = "features", label = "Features", choices = features),
+ shiny::checkboxInput(inputId = "f_func", label = "Add f()", value = FALSE),
+ shiny::actionButton(inputId = "clear", label = "Clear"),
+ ),
+ shiny::column(
+ 6,
+ shiny::h2("Formula"),
+ shiny::textOutput(outputId = "final_equation"),
+ )
  )
  ),
  shiny::tabPanel(
  "Model",
+ class = "p-3 border",
  shiny::fluidRow(
  shiny::h2("Model output"),
  # shiny::conditionalPanel("output.gotoutput", shiny::h3("Hyperparameter summary")),
@@ -248,12 +255,14 @@ model_builder_shiny <- function(spatial_data,
  ),
  shiny::tabPanel(
  "Plot",
+ class = "p-3 border",
  shiny::h2("Plot output"),
  shiny::selectInput(inputId = "plot_type", label = "Plot type:", choices = plot_choices, selected = plot_choices[1]),
  shiny::plotOutput(outputId = "plot_model_out")
  ),
  shiny::tabPanel(
  "Map",
+ class = "p-3 border",
  shiny::fluidRow(
  shiny::column(
  4,
@@ -286,11 +295,13 @@ model_builder_shiny <- function(spatial_data,
  ),
  shiny::tabPanel(
  "Code",
+ class = "p-3 border",
  shiny::selectInput(inputId = "select_run_code", label = "Select run:", choices = c()),
  shiny::verbatimTextOutput(outputId = "code_out")
  ),
  shiny::tabPanel(
  "Help",
+ class = "p-3 border",
  shiny::h3("Help"),
  shiny::h4("Spatial priors"),
  shiny::p(prior_range_text),

_pkgdown.yml

@@ -29,12 +29,10 @@ navbar:
  href: articles/simulation_poisson_data.html
  - text: ---
  - text: Shiny apps
- - text: "Map plotting"
- href: articles/mapping.html
  - text: "Mesh building"
  href: articles/meshbuilder.html
  - text: "Model builder"
- href: articles/priors_app.html
+ href: articles/modelbuilder.html
  - text: ---
  - text: In depth tutorials
  - text: "COVID-19"

vignettes/inla_FAQ.Rmd

@@ -82,3 +82,33 @@ fit.mod <- inlabru::bru(formula,
  )
 )
 ```
+
+
+## INLA error - Linux - Failed to get good enough initial values
+
+If you're running Linux and encounter an error similar to the one below:
+
+```
+.../INLA/INLA/bin/linux/64bit/inla.mkl: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by .../INLA/INLA/bin/linux/64bit/libmvec.so.1)
+
+ *** inla.core.safe: inla.program has crashed: rerun to get better initial values. try=1/1 
+Loading required package: INLA
+Warning: package 'INLA' was built under R version 4.3.1
+Loading required package: Matrix
+Loading required package: sp
+This is INLA_23.10.19-1 built 2023-10-19 08:26:30 UTC.
+ - See www.r-inla.org/contact-us for how to get help.
+ - List available models/likelihoods/etc with inla.list.models()
+ - Use inla.doc(<NAME>) to access documentation
+Warning in iinla(model = info[["model"]], lhoods = info[["lhoods"]], options = info[["options"]]) :
+ iinla: Problem in inla: Error in inla.core.safe(formula = formula, family = family, contrasts = contrasts, : 
+ *** Failed to get good enough initial values. Maybe it is due to something else.
+```
+
+You may need to run a binary install of INLA. This can be done by running the following:
+
+```{r eval=FALSE}
+INLA::inla.binary.install()
+```
+
+For more installation instructions see [the INLA documentation](https://www.r-inla.org/download-install).

vignettes/priors.Rmd

@@ -551,5 +551,5 @@ mesh <- fmesher::fm_mesh_2d_inla(
 ```
 
 ```{r eval=FALSE}
-fdmr::model_builder(spatial_data=sp_data, measurement_data = covid19_data, mesh=mesh, time_variable="week")
+fdmr::model_builder(spatial_data = sp_data, measurement_data = covid19_data, mesh = mesh, time_variable = "week")
 ```