Depositional environment: Clean original names, remove duplicates, up…

…date figures (#10)

Outputs/Tables/Table_S1.csv

@@ -1,44 +1,34 @@
 Original depositional environment,Depositional environment - broader grouping
-Lacustrine Beach,Coastal
-coastal,Coastal
-"coastal, estuarine",Coastal
-"lacustrine, playa",Coastal
+Coastal,Coastal
+"Coastal, estuarine",Coastal
+Lacustrine beach,Coastal
+"Lacustrine, playa",Coastal
 Fluvial,Fluvial
-Moraine Dammed Lake,Fluvial
-fluvial,Fluvial
+Moraine dammed lake,Fluvial
 Glacial,Glacial
-Cirque Lake,Lacustrine
-Drained Lake,Lacustrine
-Explosion Crater Lake,Lacustrine
-Glacial Origin Lake,Lacustrine
-Interdunal Lake,Lacustrine
+Cirque lake,Lacustrine
+Drained lake,Lacustrine
+Explosion crater lake,Lacustrine
+Glacial origin lake,Lacustrine
+Interdunal lake,Lacustrine
 Lacustrine,Lacustrine
-Lava Flow Dammed Lake,Lacustrine
-Natural Lake,Lacustrine
-Natural Lake (Origin Unknown),Lacustrine
-Small Hollow,Lacustrine
-Solution Origin Lake,Lacustrine
-Spring Mound,Lacustrine
-Wind Origin Lake,Lacustrine
-lacustrine,Lacustrine
-"lacustrine, drained lake",Lacustrine
-"lacustrine, natural open-water",Lacustrine
-"lacustrine, natural open-water, glacial origin",Lacustrine
-"lacustrine, natural open-water, tectonic lake",Lacustrine
-"lacustrine, volcanic lake",Lacustrine
-marine,Marine
+"Lacustrine, natural open-water",Lacustrine
+"Lacustrine, natural open-water, tectonic lake",Lacustrine
+"Lacustrine, volcanic lake",Lacustrine
+Lava flow dammed lake,Lacustrine
+Small hollow,Lacustrine
+Solution origin lake,Lacustrine
+Spring mound,Lacustrine
+Wind origin lake,Lacustrine
+Marine,Marine
 Archaeological,Terrestrial
-terrestrial,Terrestrial
-"terrestrial, cave sediments",Terrestrial
-"terrestrial, soil, buried soil",Terrestrial
-Fen,Wetlands
-Mire,Wetlands
-Swamp,Wetlands
-Valley Mire,Wetlands
-"terrestrial, mire (i.e. peatland, >30cm peat)",Wetlands
-"terrestrial, mire, bog",Wetlands
-"terrestrial, mire, bog,	blanket bog",Wetlands
-"terrestrial, mire, fen",Wetlands
-"terrestrial, mire,swamp (forested wetland or peatland)",Wetlands
+Terrestrial,Terrestrial
+"Terrestrial, cave sediments",Terrestrial
+"Terrestrial, soil, buried soil",Terrestrial
+"Terrestrial, mire",Wetlands
+"Terrestrial, mire, bog",Wetlands
+"Terrestrial, mire, bog,	blanket bog",Wetlands
+"Terrestrial, mire, fen",Wetlands
+"Terrestrial, mire, swamp",Wetlands
+Valley mire,Wetlands
 Unknown,Unknown
-NA,Unknown

R/03_Depositional_environments.R

@@ -41,6 +41,30 @@ if (
   dplyr::glimpse(data_ippd)
 }
 
+#----------------------------------------------------------#
+# 3. Remove duplicated environements -----
+#----------------------------------------------------------#
+
+data_ippd_depenv_presort <-
+  data_ippd %>%
+  dplyr::mutate(
+    depositionalenvironment = stringr::str_to_sentence(depositionalenvironment)
+  ) %>%
+  dplyr::mutate(
+    depositionalenvironment_clean = dplyr::case_when(
+      .default = depositionalenvironment,
+      depositionalenvironment == "Fen" ~ "Terrestrial, mire, fen",
+      depositionalenvironment == "Lacustrine, drained lake" ~ "Drained lake",
+      depositionalenvironment == "Lacustrine, natural open-water, glacial origin" ~ "Glacial origin lake",
+      depositionalenvironment == "Mire" ~ "Terrestrial, mire",
+      depositionalenvironment == "Natural lake" ~ "Lacustrine, natural open-water",
+      depositionalenvironment == "Natural lake (origin unknown)" ~ "Lacustrine, natural open-water",
+      depositionalenvironment == "Swamp" ~ "Terrestrial, mire, swamp",
+      depositionalenvironment == "Terrestrial, mire (i.e. peatland, >30cm peat)" ~ "Terrestrial, mire",
+      depositionalenvironment == "Terrestrial, mire,swamp (forested wetland or peatland)" ~ "Terrestrial, mire, swamp",
+      is.na(depositionalenvironment) ~ "Unknown"
+    )
+  )
 
 #----------------------------------------------------------#
 # 3. Harmonise environemnts -----
@@ -69,58 +93,50 @@ if (
 }
 
 data_ippd_depenv_harmonised <-
-  data_ippd %>%
+  data_ippd_depenv_presort %>%
   dplyr::mutate(
     depenv_harmonised = dplyr::case_when(
-      .default = depositionalenvironment,
-      depositionalenvironment %in% c(
-        "Valley Mire",
-        "Swamp",
-        "Mire",
-        "terrestrial, mire, bog,\tblanket bog",
-        "terrestrial, mire, bog",
-        "terrestrial, mire (i.e. peatland, >30cm peat)",
-        "terrestrial, mire,swamp (forested wetland or peatland)",
-        "terrestrial, mire, fen",
-        "Fen"
+      .default = depositionalenvironment_clean,
+      depositionalenvironment_clean %in% c(
+        "Valley mire",
+        "Terrestrial, mire, bog,\tblanket bog",
+        "Terrestrial, mire, bog",
+        "Terrestrial, mire",
+        "Terrestrial, mire, swamp",
+        "Terrestrial, mire, fen"
       ) ~ "Wetlands",
-      depositionalenvironment %in% c(
-        "Cirque Lake",
-        "Explosion Crater Lake",
-        "Glacial Origin Lake",
-        "Wind Origin Lake",
-        "Interdunal Lake",
-        "Natural Lake (Origin Unknown)",
-        "Lava Flow Dammed Lake",
-        "Drained Lake",
-        "Natural Lake",
-        "lacustrine, volcanic lake",
-        "lacustrine, natural open-water, tectonic lake",
-        "lacustrine, natural open-water, glacial origin",
-        "lacustrine, drained lake",
-        "Spring Mound",
-        "Small Hollow",
-        "Solution Origin Lake",
-        "lacustrine",
-        "lacustrine, natural open-water"
+      depositionalenvironment_clean %in% c(
+        "Cirque lake",
+        "Explosion crater lake",
+        "Glacial origin lake",
+        "Wind origin lake",
+        "Interdunal lake",
+        "Lava flow dammed lake",
+        "Drained lake",
+        "Lacustrine, volcanic lake",
+        "Lacustrine, natural open-water, tectonic lake",
+        "Spring mound",
+        "Small hollow",
+        "Solution origin lake",
+        "Lacustrine",
+        "Lacustrine, natural open-water"
       ) ~ "Lacustrine",
-      depositionalenvironment %in% c(
-        "Archaeological", "terrestrial, soil, buried soil",
-        "terrestrial, cave sediments",
-        "terrestrial"
+      depositionalenvironment_clean %in% c(
+        "Archaeological",
+        "Terrestrial, soil, buried soil",
+        "Terrestrial, cave sediments",
+        "Terrestrial"
       ) ~ "Terrestrial",
-      depositionalenvironment %in% c(
-        "Fluvial", "Moraine Dammed Lake",
-        "fluvial"
+      depositionalenvironment_clean %in% c(
+        "Fluvial",
+        "Moraine dammed lake"
       ) ~ "Fluvial",
-      depositionalenvironment %in% c(
-        "Lacustrine Beach",
-        "coastal, estuarine",
-        "lacustrine, playa",
-        "coastal"
-      ) ~ "Coastal",
-      depositionalenvironment == "marine" ~ "Marine",
-      is.na(depositionalenvironment) ~ "Unknown"
+      depositionalenvironment_clean %in% c(
+        "Lacustrine beach",
+        "Coastal, estuarine",
+        "Lacustrine, playa",
+        "Coastal"
+      ) ~ "Coastal"
     )
   ) %>%
   dplyr::mutate(
@@ -132,7 +148,7 @@ data_ippd_depenv_harmonised <-
 
 data_ippd_depenv_harmonised_overview <-
   data_ippd_depenv_harmonised %>%
-  dplyr::distinct(depositionalenvironment, depenv_harmonised)
+  dplyr::distinct(depositionalenvironment_clean, depenv_harmonised)
 
 assertthat::assert_that(
   data_ippd_depenv_harmonised_overview %>%
@@ -200,7 +216,7 @@ p_dep_env_main <-
 p_dep_env_bar_full <-
   plot_data_barplot(
     data = data_ippd_depenv_harmonised,
-    var_x = "depositionalenvironment",
+    var_x = "depositionalenvironment_clean",
     var_fill = "depenv_harmonised",
     y_axis_limits = c(0, 50),
     x_label_angle = 90,
@@ -306,7 +322,7 @@ purrr::walk(
 )
 
 data_ippd_depenv_harmonised_overview %>%
-  dplyr::arrange(depenv_harmonised, depositionalenvironment) %>%
+  dplyr::arrange(depenv_harmonised, depositionalenvironment_clean) %>%
   rlang::set_names(
     nm = c(
       "Original depositional environment",