🔀 Merge remote-tracking branch 'origin/feature/plot_potential_site' into develop

Author: MemoOlv

R/cli.R

@@ -31,6 +31,19 @@ plot_usage_area_by_individual <- function(options) {
   grDevices::dev.off()
 }
 
+plot_potential_site <- function(options) {
+  config_content <- read_config(options[["config-path"]])
+  trips_data <- readr::read_csv(options[["data-path"]], show_col_types = FALSE)
+  percentage_distribution <- options[["percentage-distribution"]]
+  n_iterations <- options[["n-iterations"]]
+
+  wrapper <- xxTrack2KBA_Wrapper$new(trips_data, config_content, percentage_distribution)
+  representative_assess <- wrapper$get_representative_assess(percentage_distribution, n_iterations)
+  site <- wrapper$get_potential_site(representative_assess, percentage_distribution, population_size = options[["population-size"]])
+  sf::sf_use_s2(FALSE)
+  track2KBA::mapSite(site)
+  ggplot2::ggsave(filename = options[["output-path"]], device = "png")
+}
 
 #' Plot Representative Assessment
 #'

R/representative_assess.R

@@ -50,6 +50,16 @@ xxTrack2KBA_Wrapper <- R6::R6Class(
         polyOut = FALSE
       )
       return(Site)
+    },
+    get_potential_site = function(repr, percentage_distribution, population_size) {
+      Site <- track2KBA::findSite(
+        KDE = self$KDE$KDE.Surface,
+        represent = repr$out,
+        levelUD = percentage_distribution,
+        popSize = population_size,
+        polyOut = TRUE
+      )
+      return(Site)
     }
   )
 )
@@ -105,6 +115,16 @@ Track2KBA_Wrapper <- R6::R6Class(
         polyOut = FALSE
       )
       return(Site)
+    },
+    get_potential_site = function(repr, percentage_distribution, population_size) {
+      Site <- track2KBA::findSite(
+        KDE = self$KDE$KDE.Surface,
+        represent = repr$out,
+        levelUD = percentage_distribution,
+        popSize = population_size,
+        polyOut = TRUE
+      )
+      return(Site)
     }
   )
 )

tests/testthat/test_cli.R

@@ -19,6 +19,17 @@ describe("process fisheries data", {
 })
 
 trips_path <- "/workdir/tests/data/trips_5_ids.csv"
+describe("plot potential site", {
+  output_path <- "/workdir/tests/potential_site.png"
+  options <- list("data-path" = trips_path, "config-path" = config_path, "output-path" = output_path, "percentage-distribution" = 50, "n-iterations" = 10, "population-size" = 10)
+  it("write figure", {
+    testtools::if_exist_remove(output_path)
+    plot_potential_site(options)
+    expect_true(testtools::exist_output_file(output_path))
+    testtools::if_exist_remove(output_path)
+  })
+})
+
 describe("plot ussage area by a proportion of the total birds", {
   output_path <- "/workdir/tests/usage_area.png"
   options <- list("data-path" = trips_path, "config-path" = config_path, "output-path" = output_path, "percentage-distribution" = 50, "n-iterations" = 10)