Merge pull request #30 from jzwart/final_submission_files

Final submission files
GLEON · Oct 4, 2023 · 76a4961 · 76a4961
2 parents 5f97831 + c8beebe
commit 76a4961
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Showing 27 changed files with 44 additions and 26 deletions.
diff --git a/1_plot.R b/1_plot.R
@@ -30,7 +30,7 @@ p1_targets <- list(
       metab_data = p0_metab_timeseries_data,
       season_data = p0_season_cutoff_data,
       config = p0_config,
-      out_file = "1_plot/out/fig_6_metab_timeseries_plot.png"
+      out_file = "1_plot/out/fig_5_metab_timeseries_plot.tiff"
     ),
     format = "file"
   ),
@@ -41,7 +41,7 @@ p1_targets <- list(
       load_data = p0_load_timeseries_data,
       inlake_data = p0_inlake_nutrient_timeseries_data,
       config = p0_config,
-      out_file = "1_plot/out/fig_S3_doc_timeseries_plot.png"
+      out_file = "1_plot/out/fig_S3_doc_timeseries_plot.tiff"
     ),
     format = "file"
   ),
@@ -52,7 +52,7 @@ p1_targets <- list(
       load_data = p0_load_timeseries_data,
       inlake_data = p0_inlake_nutrient_timeseries_data,
       config = p0_config,
-      out_file = "1_plot/out/fig_S1_tp_timeseries_plot.png"
+      out_file = "1_plot/out/fig_S1_tp_timeseries_plot.tiff"
     ),
     format = "file"
   ),
@@ -63,7 +63,7 @@ p1_targets <- list(
       load_data = p0_load_timeseries_data,
       inlake_data = p0_inlake_nutrient_timeseries_data,
       config = p0_config,
-      out_file = "1_plot/out/fig_S2_tn_timeseries_plot.png"
+      out_file = "1_plot/out/fig_S2_tn_timeseries_plot.tiff"
     ),
     format = "file"
   ),
@@ -73,7 +73,7 @@ p1_targets <- list(
       load_data = p0_load_timeseries_data,
       inlake_data = p0_inlake_nutrient_timeseries_data,
       config = p0_config,
-      out_file = '1_plot/out/fig_4_stoich_timeseries_plot.png'
+      out_file = '1_plot/out/fig_S4_stoich_timeseries_plot.tiff'
     ),
     format = 'file'
   ),
@@ -85,7 +85,7 @@ p1_targets <- list(
       inlake_data = p0_inlake_nutrient_timeseries_data,
       config = p0_config,
       label_id = p1_lake_label,
-      out_file = '1_plot/out/fig_2_stream_lake_nutrient_1_1.png'
+      out_file = '1_plot/out/fig_2_stream_lake_nutrient_1_1.tiff'
     ),
     format = 'file'
   ),
@@ -97,7 +97,7 @@ p1_targets <- list(
       inlake_data = p0_inlake_nutrient_timeseries_data,
       config = p0_config,
       label_id = p1_lake_label,
-      out_file = '1_plot/out/fig_3_stream_lake_stoich_scatter.png'
+      out_file = '1_plot/out/fig_3_stream_lake_stoich_scatter.tiff'
     ),
     format = 'file'
   ),
@@ -109,7 +109,7 @@ p1_targets <- list(
       inlake_data = p0_inlake_nutrient_timeseries_data,
       config = p0_config,
       label_id = p1_lake_label,
-      out_file = '1_plot/out/fig_5_plot_stoich_stream_vs_lake.png'
+      out_file = '1_plot/out/fig_4_plot_stoich_stream_vs_lake.tiff'
     )
   ),
 
@@ -118,7 +118,7 @@ p1_targets <- list(
     plot_obs_pred_metab_inlake(
       annual_data = p2_annual_data,
       label_id = p1_lake_label,
-      out_file = '1_plot/out/fig_S4_plot_obs_pred_metab_inlake.png'
+      out_file = '1_plot/out/fig_S5_plot_obs_pred_metab_inlake.tiff'
     )
   ),
 
@@ -127,7 +127,7 @@ p1_targets <- list(
     plot_obs_pred_metab_load(
       annual_data = p2_annual_data,
       label_id = p1_lake_label,
-      out_file = '1_plot/out/fig_S5_plot_obs_pred_metab_load.png'
+      out_file = '1_plot/out/fig_S6_plot_obs_pred_metab_load.tiff'
     )
   ),
 
@@ -160,7 +160,7 @@ p1_targets <- list(
     plot_models_inlake(
       annual_data = p2_annual_data,
       label_id = p1_lake_label,
-      out_file = '1_plot/out/fig_7_inlake_models.png'
+      out_file = '1_plot/out/fig_6_inlake_models.tiff'
     )
   ),
 
@@ -169,7 +169,7 @@ p1_targets <- list(
     plot_models_load(
       annual_data = p2_annual_data,
       label_id = p1_lake_label,
-      out_file = '1_plot/out/fig_8_load_models.png'
+      out_file = '1_plot/out/fig_7_load_models.tiff'
     )
   ),
 
@@ -178,7 +178,7 @@ p1_targets <- list(
     plot_doc_gpp(
       annual_data = p2_annual_data,
       label_id = p1_lake_label,
-      out_file = '1_plot/out/fig_S6_doc_gpp.png'
+      out_file = '1_plot/out/fig_S7_doc_gpp.tiff'
     )
   )
 )

diff --git a/1_plot/out/fig_2_stream_lake_nutrient_1_1.png b/1_plot/out/fig_2_stream_lake_nutrient_1_1.png
diff --git a/1_plot/out/fig_2_stream_lake_nutrient_1_1.tiff b/1_plot/out/fig_2_stream_lake_nutrient_1_1.tiff
diff --git a/1_plot/out/fig_3_stream_lake_stoich_scatter.png b/1_plot/out/fig_3_stream_lake_stoich_scatter.png
diff --git a/1_plot/out/fig_3_stream_lake_stoich_scatter.tiff b/1_plot/out/fig_3_stream_lake_stoich_scatter.tiff
diff --git a/1_plot/out/fig_4_plot_stoich_stream_vs_lake.tiff b/1_plot/out/fig_4_plot_stoich_stream_vs_lake.tiff
diff --git a/1_plot/out/fig_4_stoich_timeseries_plot.png b/1_plot/out/fig_4_stoich_timeseries_plot.png
diff --git a/1_plot/out/fig_5_metab_timeseries_plot.tiff b/1_plot/out/fig_5_metab_timeseries_plot.tiff
diff --git a/1_plot/out/fig_5_plot_stoich_stream_vs_lake.png b/1_plot/out/fig_5_plot_stoich_stream_vs_lake.png
diff --git a/1_plot/out/fig_6_inlake_models.tiff b/1_plot/out/fig_6_inlake_models.tiff
diff --git a/1_plot/out/fig_6_metab_timeseries_plot.png b/1_plot/out/fig_6_metab_timeseries_plot.png
diff --git a/1_plot/out/fig_7_inlake_models.png b/1_plot/out/fig_7_inlake_models.png
diff --git a/1_plot/out/fig_8_load_models.png b/1_plot/out/fig_8_load_models.png
diff --git a/1_plot/out/fig_S1_tp_timeseries_plot.png b/1_plot/out/fig_S1_tp_timeseries_plot.png
diff --git a/1_plot/out/fig_S1_tp_timeseries_plot.tiff b/1_plot/out/fig_S1_tp_timeseries_plot.tiff
diff --git a/1_plot/out/fig_S2_tn_timeseries_plot.png b/1_plot/out/fig_S2_tn_timeseries_plot.png
diff --git a/1_plot/out/fig_S2_tn_timeseries_plot.tiff b/1_plot/out/fig_S2_tn_timeseries_plot.tiff
diff --git a/1_plot/out/fig_S3_doc_timeseries_plot.png b/1_plot/out/fig_S3_doc_timeseries_plot.png
diff --git a/1_plot/out/fig_S3_doc_timeseries_plot.tiff b/1_plot/out/fig_S3_doc_timeseries_plot.tiff
diff --git a/1_plot/out/fig_S4_plot_obs_pred_metab_inlake.png b/1_plot/out/fig_S4_plot_obs_pred_metab_inlake.png
diff --git a/1_plot/out/fig_S4_stoich_timeseries_plot.tiff b/1_plot/out/fig_S4_stoich_timeseries_plot.tiff
diff --git a/1_plot/out/fig_S5_plot_obs_pred_metab_inlake.tiff b/1_plot/out/fig_S5_plot_obs_pred_metab_inlake.tiff
diff --git a/1_plot/out/fig_S5_plot_obs_pred_metab_load.png b/1_plot/out/fig_S5_plot_obs_pred_metab_load.png
diff --git a/1_plot/out/fig_S6_doc_gpp.png b/1_plot/out/fig_S6_doc_gpp.png
diff --git a/1_plot/out/fig_S6_plot_obs_pred_metab_load.tiff b/1_plot/out/fig_S6_plot_obs_pred_metab_load.tiff
diff --git a/1_plot/out/fig_S7_doc_gpp.tiff b/1_plot/out/fig_S7_doc_gpp.tiff
diff --git a/1_plot/src/plotting_functions.R b/1_plot/src/plotting_functions.R
@@ -71,7 +71,8 @@ plot_metab_timeseries <- function(
   ggsave(out_file,
          plot = metab,
          width = 10,
-         height = 10)
+         height = 10,
+         dpi = 400)
 }
 
 
@@ -153,7 +154,8 @@ plot_doc_timeseries <- function(
 
   ggsave(out_file,
          plot = doc_load,
-         width = 10, height = 10)
+         width = 10, height = 10,
+         dpi = 400)
 }
 
 plot_tn_timeseries <- function(
@@ -234,7 +236,8 @@ plot_tn_timeseries <- function(
 
   ggsave(out_file,
          plot = tn_load,
-         width = 10, height = 10)
+         width = 10, height = 10,
+         dpi = 400)
 }
 
 
@@ -316,7 +319,8 @@ plot_tp_timeseries <- function(
 
   ggsave(out_file,
          plot = tp_load,
-         width = 10, height = 10)
+         width = 10, height = 10,
+         dpi = 400)
 }
 
 
@@ -485,7 +489,8 @@ plot_stoich_timeseries <- function(
 
   ggsave(out_file,
          plot = lake_load_stoich,
-         width = 10, height = 10)
+         width = 10, height = 10,
+         dpi = 400)
 }
 
 
@@ -627,7 +632,8 @@ plot_stream_lake_nutrient <- function(
 
   ggsave(out_file,
          plot = g,
-         width = 12, height = 4)
+         width = 12, height = 4,
+         dpi = 400)
   return(out_file)
 }
 
@@ -992,7 +998,8 @@ plot_stream_lake_stoich_scatter <- function(
   browser()
   ggsave(out_file,
          plot = g,
-         width = 12, height = 8)
+         width = 12, height = 8,
+         dpi = 400)
   return(out_file)
 }
 
@@ -1178,7 +1185,8 @@ plot_stoich_stream_vs_lake <- function(
 
   ggsave(out_file,
          plot = g,
-         width = 12, height = 4)
+         width = 12, height = 4,
+         dpi = 400)
   return(out_file)
 }
 
@@ -1262,7 +1270,9 @@ plot_obs_pred_metab_inlake <- function(
   plot_out = cowplot::plot_grid(gpp, r, nep, nrow = 1)
 
   ggsave(filename = out_file,
-         plot = plot_out, width = 14, height =5 )
+         plot = plot_out,
+         width = 14, height =5,
+         dpi = 400)
 
   return(out_file)
 }
@@ -1449,7 +1459,9 @@ plot_obs_pred_metab_load <- function(
   plot_out = cowplot::plot_grid(gpp, r, nep, nrow = 1)
 
   ggsave(filename = out_file,
-         plot = plot_out, width = 14, height =5 )
+         plot = plot_out,
+         width = 14, height =5,
+         dpi = 400)
 
   return(out_file)
 }
@@ -1647,7 +1659,9 @@ plot_models_inlake <- function(
                                            "D", "E"))
 
   ggsave(filename = out_file,
-         plot = plot_out, width = 9, height = 14 )
+         plot = plot_out,
+         width = 9, height = 14,
+         dpi = 350)
 
   return(out_file)
 }
@@ -1816,7 +1830,9 @@ plot_models_load <- function(
                                            "G", "", ""))
 
   ggsave(filename = out_file,
-         plot = plot_out, width = 16, height = 16 )
+         plot = plot_out,
+         width = 16, height = 16,
+         dpi = 300)
 
   return(out_file)
 }
@@ -1872,7 +1888,9 @@ plot_doc_gpp <- function(
     ggrepel::geom_text_repel(aes(label=label_id))
 
   ggsave(filename = out_file,
-         plot = gpp, width = 6, height = 6)
+         plot = gpp,
+         width = 6, height = 6,
+         dpi = 400)
 
   return(out_file)
 }