Merge pull request #112 from AgrDataSci/devel

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AgrDataSci · Jun 5, 2023 · b2750f0 · b2750f0
2 parents 5cad87d + f0162bd
commit b2750f0
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Showing 2 changed files with 34 additions and 7 deletions.
diff --git a/modules/05_spatial_overview.R b/modules/05_spatial_overview.R
@@ -64,9 +64,10 @@ get_testing_sites_map = function(cmdata, output_path, backward_path){
 
     dir.create(tempmap, recursive = TRUE, showWarnings = FALSE)
 
-    mapview::mapshot(trial_map, 
+    try(mapview::mapshot(trial_map, 
                      url = paste0(tempmap, "/trial_map.html"),
-                     file = paste0(tempmap, "/trial_map.png"))
+                     file = paste0(tempmap, "/trial_map.png")),
+        silent = TRUE)
 
   }
 

diff --git a/modules/10_quantitative_insights.R b/modules/10_quantitative_insights.R
@@ -4,6 +4,28 @@
 #' retained in the quanti_dat object
 #' 
 #' @param quanti_dat a list with parameters
+#' @examples 
+#' modules = list.files("modules", full.names = TRUE,pattern = ".R")
+#' 
+#' modules = modules[-which(grepl("check_packages.R", modules))]
+#' for (i in seq_along(modules)) {
+#'   source(modules[i])
+#' }
+#' 
+#' load("modules/example-data-structure.rda")
+#' 
+#' # ClimMob parameters
+#' pars = decode_pars(cmpars)
+#' 
+#' quanti_dat =  organize_quantitative_data(cmdata,
+#'                                          pars,
+#'                                          groups = "gender1",
+#'                                          id = "id",
+#'                                          tech_index = paste0("package_item_", LETTERS[1:3]))
+#' 
+#' 
+#' get_quantitative_summaries(quanti_dat)
+#' @export
 get_quantitative_summaries <- function(quanti_dat) {
 
   # make density plots with the data 
@@ -16,18 +38,22 @@ get_quantitative_summaries <- function(quanti_dat) {
 
     ggdat_i <- quanti_dat$quanti_dat[[i]]
 
-    b_i <- ggplot(ggdat_i, aes(y = value, x = technology, color = technology)) +
-      geom_boxplot(show.legend = FALSE) +
-      geom_jitter(show.legend = FALSE) +
-      scale_color_brewer(palette = "BrBG", name = "") +
+    b_i <- ggplot(ggdat_i, aes(x = value, 
+                               y = technology, 
+                               color = "#006d2c")) +
+      geom_boxplot(show.legend = FALSE,
+                   outlier.colour = "#d95f02") +
+
+      #geom_jitter(show.legend = FALSE, color = "#006d2c") +
+      scale_color_manual(values = "#006d2c") +
       labs(title = paste(unique(ggdat_i$trait), unique(ggdat_i$data_collection), sep = " - "),
            x = "",
            y = "") +
       theme_bw() + 
       theme(panel.grid = element_blank(),
             text = element_text(size = 16),
             title = element_text(size = 12),
-            axis.text.x = element_text(angle = 45,  hjust = 1))
+            axis.text.x = element_text(angle = 0,  hjust = 0.5))
 
     densitplots[[i]] <- b_i
     density_file_names[[i]] <- tolower(gsub(" ", "",