1. Priors Shiny App

DESCRIPTION

@@ -49,7 +49,8 @@ Imports:
     leaflet,
     archive,
     shiny,
-    stringr
+    stringr,
+    shinybusy
 Suggests: 
     bookdown,
     knitr,

NAMESPACE

@@ -2,12 +2,14 @@
 
 export(clear_caches)
 export(get_tutorial_datapath)
+export(interactive_priors)
 export(latlong_to_utm)
 export(load_tutorial_data)
 export(mesh_builder)
 export(mesh_checker)
 export(mesh_to_spatial)
 export(numbers_only)
+export(parse_model_output)
 export(plot_barchart)
 export(plot_boxplot)
 export(plot_interactive_map)
@@ -17,4 +19,5 @@ export(plot_mesh)
 export(plot_timeseries)
 export(retrieve_tutorial_data)
 export(to_dates)
+importFrom(INLA,f)
 importFrom(magrittr,"%>%")

R/model_parse.R

@@ -0,0 +1,45 @@
+#' Parses inlabru::bru model output
+#'
+#' @param model_output Output from running inlabru::bru
+#' @param measurement_data Measurement data
+#'
+#' @return list
+#' @keywords internal
+parse_model_output_bru <- function(model_output, measurement_data) {
+    fitted_mean_post <- model_output$summary.fitted.values$mean[seq_len(nrow(measurement_data))]
+    fitted_sd_post <- model_output$summary.fitted.values$mean[seq_len(nrow(measurement_data))]
+
+    mean_post <- model_output$summary.random$f$mean
+    sd_post <- model_output$summary.random$f$sd
+    fixed_mean <- model_output$summary.fixed$mean
+
+    dic <- model_output$dic$dic
+    pars <- model_output$marginals.hyperpar
+
+    parsed_output <- list(
+        fitted_mean_post = fitted_mean_post,
+        fitted_sd_post = fitted_sd_post,
+        mean_post = mean_post,
+        sd_post = sd_post,
+        fixed_mean = fixed_mean,
+        dic = dic,
+        pars = pars
+    )
+
+    return(parsed_output)
+}
+
+
+#' Parse model output
+#'
+#' @param model_output Data returned by model
+#' @param measurement_data Measurement data
+#' @param model_type Type of model, we currently support inlabru
+#'
+#' @return list
+#' @export
+parse_model_output <- function(model_output, measurement_data, model_type = "inlabru") {
+    if (model_type == "inlabru") {
+        return(parse_model_output_bru(model_output = model_output, measurement_data = measurement_data))
+    }
+}

R/plot_mapping.R

@@ -48,6 +48,7 @@ plot_map <- function(polygon_data = NULL,
         title = legend_title
       )
     }
+
     m <- leaflet::addPolygons(m,
       data = polygon_data,
       fillColor = polygon_fill_colour,