UGH i hate figures

diazrenata · May 8, 2021 · 44fd44e · 44fd44e
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diff --git a/...ission2/appendices/graphical_abstract.pdf → ...t/Appendices/ELEDiazGraphicalAbstract.pdf b/...ission2/appendices/graphical_abstract.pdf → ...t/Appendices/ELEDiazGraphicalAbstract.pdf
diff --git a/analysis/manuscript/finaledit/Appendices/ELEDiazSA1.docx b/analysis/manuscript/finaledit/Appendices/ELEDiazSA1.docx
diff --git a/...n2/appendices/s10_very_small_results.docx → ...ipt/finaledit/Appendices/ELEDiazSA10.docx b/...n2/appendices/s10_very_small_results.docx → ...ipt/finaledit/Appendices/ELEDiazSA10.docx
diff --git a/analysis/manuscript/finaledit/Appendices/ELEDiazSA2.docx b/analysis/manuscript/finaledit/Appendices/ELEDiazSA2.docx
diff --git a/analysis/manuscript/finaledit/Appendices/ELEDiazSA3.docx b/analysis/manuscript/finaledit/Appendices/ELEDiazSA3.docx
diff --git a/...dices/s7_complete_resampling_results.docx → ...ript/finaledit/Appendices/ELEDiazSA7.docx b/...dices/s7_complete_resampling_results.docx → ...ript/finaledit/Appendices/ELEDiazSA7.docx
diff --git a/...rts/submission2/appendices/s8_gentry.docx → ...ript/finaledit/Appendices/ELEDiazSA8.docx b/...rts/submission2/appendices/s8_gentry.docx → ...ript/finaledit/Appendices/ELEDiazSA8.docx
diff --git a/...ission2/appendices/s9_fia_comparison.docx → ...ript/finaledit/Appendices/ELEDiazSA9.docx b/...ission2/appendices/s9_fia_comparison.docx → ...ript/finaledit/Appendices/ELEDiazSA9.docx
diff --git a/...ion2/appendices/s4_dissimilarity_fig.docx → ...ript/finaledit/Appendices/ELEDiazSF4.docx b/...ion2/appendices/s4_dissimilarity_fig.docx → ...ript/finaledit/Appendices/ELEDiazSF4.docx
diff --git a/...ion2/appendices/s6_breadth_index_fig.docx → ...ript/finaledit/Appendices/ELEDiazSF6.docx b/...ion2/appendices/s6_breadth_index_fig.docx → ...ript/finaledit/Appendices/ELEDiazSF6.docx
diff --git a/...endices/s5_results_unusual_direction.docx → ...ript/finaledit/Appendices/ELEDiazST5.docx b/...endices/s5_results_unusual_direction.docx → ...ript/finaledit/Appendices/ELEDiazST5.docx
diff --git a/analysis/manuscript/finaledit/FiguresAndTables/FigureLegends.docx b/analysis/manuscript/finaledit/FiguresAndTables/FigureLegends.docx
diff --git a/analysis/reports/submission2/figure_1.pdf → ...t/finaledit/FiguresAndTables/figure_1.pdf b/analysis/reports/submission2/figure_1.pdf → ...t/finaledit/FiguresAndTables/figure_1.pdf
diff --git a/analysis/reports/submission2/figure_2.pdf → ...t/finaledit/FiguresAndTables/figure_2.pdf b/analysis/reports/submission2/figure_2.pdf → ...t/finaledit/FiguresAndTables/figure_2.pdf
diff --git a/...orts/submission2/figure_2_second_copy.pdf → ...FiguresAndTables/figure_2_second_copy.pdf b/...orts/submission2/figure_2_second_copy.pdf → ...FiguresAndTables/figure_2_second_copy.pdf
diff --git a/analysis/reports/submission2/figure_3.pdf → ...t/finaledit/FiguresAndTables/figure_3.pdf b/analysis/reports/submission2/figure_3.pdf → ...t/finaledit/FiguresAndTables/figure_3.pdf
diff --git a/analysis/reports/submission2/figure_4.pdf → ...t/finaledit/FiguresAndTables/figure_4.pdf b/analysis/reports/submission2/figure_4.pdf → ...t/finaledit/FiguresAndTables/figure_4.pdf
diff --git a/analysis/reports/submission2/figure_5.pdf → ...t/finaledit/FiguresAndTables/figure_5.pdf b/analysis/reports/submission2/figure_5.pdf → ...t/finaledit/FiguresAndTables/figure_5.pdf
diff --git a/analysis/reports/submission2/figure_6.pdf → ...t/finaledit/FiguresAndTables/figure_6.pdf b/analysis/reports/submission2/figure_6.pdf → ...t/finaledit/FiguresAndTables/figure_6.pdf
diff --git a/analysis/manuscript/finaledit/FiguresAndTables/table_1.docx b/analysis/manuscript/finaledit/FiguresAndTables/table_1.docx
diff --git a/analysis/manuscript/finaledit/MainText_final_ele.docx b/analysis/manuscript/finaledit/MainText_final_ele.docx
diff --git a/analysis/manuscript/revision1/MainTextR1_biorxiv.docx b/analysis/manuscript/revision1/MainTextR1_biorxiv.docx
diff --git a/analysis/manuscript/revision1/MainTextR1_biorxiv.pdf b/analysis/manuscript/revision1/MainTextR1_biorxiv.pdf
diff --git a/analysis/reports/submission2/all_ct.csv → analysis/reports/finaledit/all_ct.csv b/analysis/reports/submission2/all_ct.csv → analysis/reports/finaledit/all_ct.csv
diff --git a/analysis/reports/submission2/all_ct_jk.csv → analysis/reports/finaledit/all_ct_jk.csv b/analysis/reports/submission2/all_ct_jk.csv → analysis/reports/finaledit/all_ct_jk.csv
diff --git a/analysis/reports/submission2/all_di.csv → analysis/reports/finaledit/all_di.csv b/analysis/reports/submission2/all_di.csv → analysis/reports/finaledit/all_di.csv
diff --git a/...is/reports/submission2/all_di_columns.csv → ...ysis/reports/finaledit/all_di_columns.csv b/...is/reports/submission2/all_di_columns.csv → ...ysis/reports/finaledit/all_di_columns.csv
diff --git a/...s/reports/submission2/all_di_columns.xlsx → ...sis/reports/finaledit/all_di_columns.xlsx b/...s/reports/submission2/all_di_columns.xlsx → ...sis/reports/finaledit/all_di_columns.xlsx
diff --git a/analysis/reports/submission2/all_di_jk.csv → analysis/reports/finaledit/all_di_jk.csv b/analysis/reports/submission2/all_di_jk.csv → analysis/reports/finaledit/all_di_jk.csv
diff --git a/...ission2/appendices/graphical_abstract.Rmd → ...naledit/appendices/graphical_abstract.Rmd b/...ission2/appendices/graphical_abstract.Rmd → ...naledit/appendices/graphical_abstract.Rmd
diff --git a/...mission2/appendices/graphical_abstract.md → ...inaledit/appendices/graphical_abstract.md b/...mission2/appendices/graphical_abstract.md → ...inaledit/appendices/graphical_abstract.md
diff --git a/analysis/reports/finaledit/appendices/graphical_abstract.pdf b/analysis/reports/finaledit/appendices/graphical_abstract.pdf
diff --git a/...ct_files/figure-gfm/unnamed-chunk-2-1.png → ...ct_files/figure-gfm/unnamed-chunk-2-1.png b/...ct_files/figure-gfm/unnamed-chunk-2-1.png → ...ct_files/figure-gfm/unnamed-chunk-2-1.png
diff --git a/...orts/submission2/appendices/portal_di.csv → ...eports/finaledit/appendices/portal_di.csv b/...orts/submission2/appendices/portal_di.csv → ...eports/finaledit/appendices/portal_di.csv
diff --git a/...submission2/appendices/portal_samples.csv → ...s/finaledit/appendices/portal_samples.csv b/...submission2/appendices/portal_samples.csv → ...s/finaledit/appendices/portal_samples.csv
diff --git a/...on2/appendices/s10_very_small_results.Rmd → ...dit/appendices/s10_very_small_results.Rmd b/...on2/appendices/s10_very_small_results.Rmd → ...dit/appendices/s10_very_small_results.Rmd
@@ -292,9 +292,9 @@ Breadth indices (top) and percentile scores (bottom) for communities with fewer
 
 ```{r, fig.dim = c(6,8)}
 
-nhist <- plot_narrowness_hist(filter(all_di, dat %in% c("fia", "mcdb", "misc_abund")), "sim_pos_from_best", "Dissimilarity to the central tendency") +
+nhist <- plot_narrowness_hist(filter(all_di, dat %in% c("fia", "mcdb", "misc_abund")), "sim_pos_from_best_95", "Dissimilarity to the central tendency") +
   facet_wrap(vars(`Number of elements`, Dataset), scales = "free_y", nrow = 2, ncol = 3) +
-  xlab("Mean dissimilarity of elements of feasible set to central tendency") +
+  xlab("95th percentile of scores for dissimilarity to the central tendency \nfor elements of the feasible set") +
   ylab("Number of communities") +
   ggtitle("")
 

diff --git a/analysis/reports/finaledit/appendices/s10_very_small_results.docx b/analysis/reports/finaledit/appendices/s10_very_small_results.docx
diff --git a/...ion2/appendices/s10_very_small_results.md → ...edit/appendices/s10_very_small_results.md b/...ion2/appendices/s10_very_small_results.md → ...edit/appendices/s10_very_small_results.md
diff --git a/...ts_files/figure-gfm/unnamed-chunk-5-1.png → ...ts_files/figure-gfm/unnamed-chunk-5-1.png b/...ts_files/figure-gfm/unnamed-chunk-5-1.png → ...ts_files/figure-gfm/unnamed-chunk-5-1.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-5-2.png → ...ts_files/figure-gfm/unnamed-chunk-5-2.png b/...ts_files/figure-gfm/unnamed-chunk-5-2.png → ...ts_files/figure-gfm/unnamed-chunk-5-2.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-5-3.png → ...ts_files/figure-gfm/unnamed-chunk-5-3.png b/...ts_files/figure-gfm/unnamed-chunk-5-3.png → ...ts_files/figure-gfm/unnamed-chunk-5-3.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-5-4.png → ...ts_files/figure-gfm/unnamed-chunk-5-4.png b/...ts_files/figure-gfm/unnamed-chunk-5-4.png → ...ts_files/figure-gfm/unnamed-chunk-5-4.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-5-5.png → ...ts_files/figure-gfm/unnamed-chunk-5-5.png b/...ts_files/figure-gfm/unnamed-chunk-5-5.png → ...ts_files/figure-gfm/unnamed-chunk-5-5.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-7-1.png → ...ts_files/figure-gfm/unnamed-chunk-7-1.png b/...ts_files/figure-gfm/unnamed-chunk-7-1.png → ...ts_files/figure-gfm/unnamed-chunk-7-1.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-7-2.png → ...ts_files/figure-gfm/unnamed-chunk-7-2.png b/...ts_files/figure-gfm/unnamed-chunk-7-2.png → ...ts_files/figure-gfm/unnamed-chunk-7-2.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-7-3.png → ...ts_files/figure-gfm/unnamed-chunk-7-3.png b/...ts_files/figure-gfm/unnamed-chunk-7-3.png → ...ts_files/figure-gfm/unnamed-chunk-7-3.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-7-4.png → ...ts_files/figure-gfm/unnamed-chunk-7-4.png b/...ts_files/figure-gfm/unnamed-chunk-7-4.png → ...ts_files/figure-gfm/unnamed-chunk-7-4.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-7-5.png → ...ts_files/figure-gfm/unnamed-chunk-7-5.png b/...ts_files/figure-gfm/unnamed-chunk-7-5.png → ...ts_files/figure-gfm/unnamed-chunk-7-5.png
diff --git a/...sion2/appendices/s4_dissimilarity_fig.Rmd → ...ledit/appendices/s4_dissimilarity_fig.Rmd b/...sion2/appendices/s4_dissimilarity_fig.Rmd → ...ledit/appendices/s4_dissimilarity_fig.Rmd
@@ -110,7 +110,7 @@ ggplot(all_di, aes(sim_pos_from_best, real_po, color = `Observed \npercentile sc
   geom_point(data = filter(all_di, s0 < 0)) +
   geom_abline(slope = 1, intercept = 0) +
   scale_color_viridis_d(end = .8, direction = -1) +
-  xlab("Mean of elements from feasible set") +
+  xlab("Mean for elements from feasible set") +
   ylab("Observed value") +
   ggtitle("Dissimilarity to the central tendency") +  theme(legend.position = "bottom")+
   facet_wrap(vars(Dataset))

diff --git a/analysis/reports/finaledit/appendices/s4_dissimilarity_fig.docx b/analysis/reports/finaledit/appendices/s4_dissimilarity_fig.docx
diff --git a/...ssion2/appendices/s4_dissimilarity_fig.md → ...aledit/appendices/s4_dissimilarity_fig.md b/...ssion2/appendices/s4_dissimilarity_fig.md → ...aledit/appendices/s4_dissimilarity_fig.md
diff --git a/...ig_files/figure-gfm/unnamed-chunk-2-1.png → ...ig_files/figure-gfm/unnamed-chunk-2-1.png b/...ig_files/figure-gfm/unnamed-chunk-2-1.png → ...ig_files/figure-gfm/unnamed-chunk-2-1.png
diff --git a/...pendices/s5_results_unusual_direction.Rmd → ...pendices/s5_results_unusual_direction.Rmd b/...pendices/s5_results_unusual_direction.Rmd → ...pendices/s5_results_unusual_direction.Rmd
diff --git a/analysis/reports/finaledit/appendices/s5_results_unusual_direction.docx b/analysis/reports/finaledit/appendices/s5_results_unusual_direction.docx
diff --git a/...sion2/appendices/s6_breadth_index_fig.Rmd → ...ledit/appendices/s6_breadth_index_fig.Rmd b/...sion2/appendices/s6_breadth_index_fig.Rmd → ...ledit/appendices/s6_breadth_index_fig.Rmd
@@ -169,7 +169,7 @@ plot_narrowness_hist <- function(di_df, col_name, plot_name, facetvar = "Dataset
 
 fig_2 <- gridExtra::grid.arrange(grobs = list(
 
-  plot_narrowness_hist(all_di, "sim_pos_from_best", "Dissimilarity to the \ncentral tendency", facetvar = "Dataset"),
+  plot_narrowness_hist(all_di, "sim_pos_from_best_95", "Dissimilarity to the \ncentral tendency", facetvar = "Dataset"),
   plot_narrowness_hist(all_di, "nsingletons_95_ratio_2t", "\nNumber of rare species", facetvar = "Dataset"),
   plot_narrowness_hist(all_di, "skew_95_ratio_2t", "\nSkewness", facetvar = "Dataset", min_s0 = 3),
   plot_narrowness_hist(all_di, "simpson_95_ratio_2t", "\nSimpson evenness", facetvar = "Dataset"),
@@ -181,4 +181,4 @@ fig_2 <- gridExtra::grid.arrange(grobs = list(
 ```
 
 
-**Figure S6**. Partially because of the uneven distribution of S and N among the different datasets, the narrowness of the feasible sets - defined either as the mean dissimilarity of samples from the feasible set to the central tendency of the feasible set, or using a breadth index for specific metrics - varies among different datasets. In particular, the FIA dataset, and subsets of the Mammal Community and Miscellaneous Abundance databases, often have highly variable, broadly-defined statistical baselines derived from the feasible set. 
+**Figure S6**. Partially because of the uneven distribution of S and N among the different datasets, the narrowness of the feasible sets - defined either as the 95th percentile of scores for the dissimilarity of samples from the feasible set to the central tendency of the feasible set, or using a breadth index for specific metrics - varies among different datasets. In particular, the FIA dataset, and subsets of the Mammal Community and Miscellaneous Abundance databases, often have highly variable, broadly-defined statistical baselines derived from the feasible set. 
diff --git a/analysis/reports/finaledit/appendices/s6_breadth_index_fig.docx b/analysis/reports/finaledit/appendices/s6_breadth_index_fig.docx
diff --git a/...ndices/s7_complete_resampling_results.Rmd → ...ndices/s7_complete_resampling_results.Rmd b/...ndices/s7_complete_resampling_results.Rmd → ...ndices/s7_complete_resampling_results.Rmd
diff --git a/analysis/reports/finaledit/appendices/s7_complete_resampling_results.docx b/analysis/reports/finaledit/appendices/s7_complete_resampling_results.docx
diff --git a/...endices/s7_complete_resampling_results.md → ...endices/s7_complete_resampling_results.md b/...endices/s7_complete_resampling_results.md → ...endices/s7_complete_resampling_results.md
diff --git a/...ts_files/figure-gfm/unnamed-chunk-5-1.png → ...ts_files/figure-gfm/unnamed-chunk-5-1.png b/...ts_files/figure-gfm/unnamed-chunk-5-1.png → ...ts_files/figure-gfm/unnamed-chunk-5-1.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-5-2.png → ...ts_files/figure-gfm/unnamed-chunk-5-2.png b/...ts_files/figure-gfm/unnamed-chunk-5-2.png → ...ts_files/figure-gfm/unnamed-chunk-5-2.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-6-1.png → ...ts_files/figure-gfm/unnamed-chunk-6-1.png b/...ts_files/figure-gfm/unnamed-chunk-6-1.png → ...ts_files/figure-gfm/unnamed-chunk-6-1.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-6-2.png → ...ts_files/figure-gfm/unnamed-chunk-6-2.png b/...ts_files/figure-gfm/unnamed-chunk-6-2.png → ...ts_files/figure-gfm/unnamed-chunk-6-2.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-7-1.png → ...ts_files/figure-gfm/unnamed-chunk-7-1.png b/...ts_files/figure-gfm/unnamed-chunk-7-1.png → ...ts_files/figure-gfm/unnamed-chunk-7-1.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-8-1.png → ...ts_files/figure-gfm/unnamed-chunk-8-1.png b/...ts_files/figure-gfm/unnamed-chunk-8-1.png → ...ts_files/figure-gfm/unnamed-chunk-8-1.png
diff --git a/...ts_files/figure-gfm/unnamed-chunk-9-1.png → ...ts_files/figure-gfm/unnamed-chunk-9-1.png b/...ts_files/figure-gfm/unnamed-chunk-9-1.png → ...ts_files/figure-gfm/unnamed-chunk-9-1.png
diff --git a/...orts/submission2/appendices/s8_gentry.Rmd → ...eports/finaledit/appendices/s8_gentry.Rmd b/...orts/submission2/appendices/s8_gentry.Rmd → ...eports/finaledit/appendices/s8_gentry.Rmd
diff --git a/analysis/reports/finaledit/appendices/s8_gentry.docx b/analysis/reports/finaledit/appendices/s8_gentry.docx
diff --git a/...mission2/appendices/s9_fia_comparison.Rmd → ...inaledit/appendices/s9_fia_comparison.Rmd b/...mission2/appendices/s9_fia_comparison.Rmd → ...inaledit/appendices/s9_fia_comparison.Rmd
@@ -407,7 +407,7 @@ bind_rows(simpson_perc_ks, skew_perc_ks, shannon_perc_ks, nsingletons_perc_ks, d
 ```{r, fig.dim = c(8,4)}
 fig_2 <- gridExtra::grid.arrange(grobs = list(
 
-  plot_narrowness_hist(sub_di, "sim_pos_from_best", "Dissimilarity to the \ncentral tendency", facetvar = "Dataset"),
+  plot_narrowness_hist(sub_di, "sim_pos_from_best_95", "Dissimilarity to the \ncentral tendency", facetvar = "Dataset"),
   plot_narrowness_hist(sub_di, "nsingletons_95_ratio_2t", "\nNumber of rare species", facetvar = "Dataset"),
   plot_narrowness_hist(sub_di, "skew_95_ratio_2t", "\nSkewness", facetvar = "Dataset", min_s0 = 3),
   plot_narrowness_hist(sub_di, "simpson_95_ratio_2t", "\nSimpson evenness", facetvar = "Dataset"),
@@ -424,7 +424,7 @@ simpson_rat_ks <- ks_compare(fia_di, other_di, "simpson_95_ratio_2t")
 skew_rat_ks <- ks_compare(fia_di, other_di, "skew_95_ratio_2t")
 shannon_rat_ks <- ks_compare(fia_di, other_di, "shannon_95_ratio_2t")
 nsingletons_rat_ks <- ks_compare(fia_di, other_di, "nsingletons_95_ratio_2t")
-diss_rat_ks <- ks_compare(fia_di, other_di, "sim_pos_from_best")
+diss_rat_ks <- ks_compare(fia_di, other_di, "sim_pos_from_best_95")
 
 bind_rows(simpson_rat_ks, skew_rat_ks, shannon_rat_ks, nsingletons_rat_ks, diss_rat_ks) %>%
   select(var, d, p) %>%

diff --git a/analysis/reports/finaledit/appendices/s9_fia_comparison.docx b/analysis/reports/finaledit/appendices/s9_fia_comparison.docx
diff --git a/...bmission2/appendices/s9_fia_comparison.md → ...finaledit/appendices/s9_fia_comparison.md b/...bmission2/appendices/s9_fia_comparison.md → ...finaledit/appendices/s9_fia_comparison.md
diff --git a/...on_files/figure-gfm/unnamed-chunk-5-1.png → ...on_files/figure-gfm/unnamed-chunk-5-1.png b/...on_files/figure-gfm/unnamed-chunk-5-1.png → ...on_files/figure-gfm/unnamed-chunk-5-1.png
diff --git a/...on_files/figure-gfm/unnamed-chunk-8-1.png → ...on_files/figure-gfm/unnamed-chunk-8-1.png b/...on_files/figure-gfm/unnamed-chunk-8-1.png → ...on_files/figure-gfm/unnamed-chunk-8-1.png
diff --git a/...bmission2/appendices/style_reference.docx → ...finaledit/appendices/style_reference.docx b/...bmission2/appendices/style_reference.docx → ...finaledit/appendices/style_reference.docx
diff --git a/analysis/reports/finaledit/figure_1.pdf b/analysis/reports/finaledit/figure_1.pdf
diff --git a/analysis/reports/finaledit/figure_2.pdf b/analysis/reports/finaledit/figure_2.pdf
diff --git a/analysis/reports/finaledit/figure_2_second_copy.pdf b/analysis/reports/finaledit/figure_2_second_copy.pdf
diff --git a/analysis/reports/finaledit/figure_3.pdf b/analysis/reports/finaledit/figure_3.pdf
diff --git a/analysis/reports/finaledit/figure_4.pdf b/analysis/reports/finaledit/figure_4.pdf
diff --git a/analysis/reports/finaledit/figure_5.pdf b/analysis/reports/finaledit/figure_5.pdf
diff --git a/analysis/reports/finaledit/figure_6.pdf b/analysis/reports/finaledit/figure_6.pdf
diff --git a/...ports/submission2/manuscript_main_rev.Rmd → ...reports/finaledit/manuscript_main_rev.Rmd b/...ports/submission2/manuscript_main_rev.Rmd → ...reports/finaledit/manuscript_main_rev.Rmd
@@ -74,19 +74,12 @@ fig1 <- ggplot(all_di, aes(x = s0, y = n0, color = Dataset)) +
   xlab("Species richness (S); note log scale") +
   ylab("Total abundance (N); note log scale") +
   scale_x_log10() +
-  scale_y_log10() 
+  scale_y_log10()  +
+  theme(legend.position = c(.3,.8), legend.justification = "center", legend.background = element_blank(), legend.text	= element_text(size = 8), legend.title = element_text(size = 9), legend.key.size = unit(2, units = "mm"), axis.text = element_text(size = 7))
 
 
-fig1_with_top = gridExtra::grid.arrange(grobs = list(fig1), 
-top = textGrob("Figure 1"))
 
-# 
-# pdf("figure_1.pdf", bg = "white", paper = "letter", width = 6.5, height = 6.5)
-# gridExtra::grid.arrange(grobs = list(fig1), 
-# top = textGrob("Figure 1"))
-# dev.off()
-
-ggsave("figure_1.pdf", plot = fig1_with_top, device = "pdf", width = 6.5, height = 6.5, units = "in")
+ggsave("figure_1.pdf", plot = fig1, device = "pdf", width = 80, height = 80, units = "mm")
 
 
 ```
@@ -196,13 +189,13 @@ breadth_plots <- list(
 
 )
 
-fig_2 <- gridExtra::grid.arrange(grobs = breadth_plots, ncol = 2, top = textGrob("Figure 2", gp = gpar(fill = "white")))
-
-ggsave("figure_2.pdf", plot = fig_2, device = "pdf", width = 8, height = 8, units = "in")
+fig_2 <- gridExtra::grid.arrange(grobs = breadth_plots, ncol = 2)
 
-signif(as.numeric(example_di$nparts), digits = 2)
-(as.numeric(example_di2$nparts))
-as.numeric(example_di3$nparts)
+ggsave("figure_2.pdf", plot = fig_2, device = "pdf", width = 180, height = 180, dpi = 800, units = "mm")
+# 
+signif(as.numeric(example_di$nparts), digits = 2)[1]
+(as.numeric(example_di2$nparts))[1]
+as.numeric(example_di3$nparts)[1]
 
 DBI::dbDisconnect(db)
 rm(cache)
@@ -228,14 +221,16 @@ plot_percentile_hist <- function(di_df, col_name, plot_name, tails = 2, facetvar
 
 
   ggplot(filter(di_df, nparts > min_nparts, s0 >= min_s0), aes(response)) +
-    geom_histogram(bins = 40, boundary = 100) +
+    geom_histogram(bins = 100, boundary = 100) +
     theme_bw() +
     xlab("") +
     ylab("") +
     geom_vline(xintercept = cutoff_percentiles, color = "red") +
     ggtitle( plot_name) +
+    #geom_text(data = distinct(select(di_df, Dataset)), aes(x = 45, y = 100, label = Dataset)) +
     facet_wrap(vars(facetvar), ncol = 1, scales = "free_y")+
-    theme(plot.title = element_text(size=10))
+    theme(plot.title = element_text(size=9), plot.margin=unit(c(1, 0, -5, -3), units = "mm"), axis.text = element_text(size = 6), strip.text = element_text(size = 7), strip.placement = "inside") +
+    scale_y_continuous(n.breaks = 3)
 
 
 
@@ -256,25 +251,20 @@ all_di <- all_di %>%
 
 fig_3 <- gridExtra::grid.arrange(grobs = list(
 
-  plot_percentile_hist(all_di, "real_po_percentile_mean", "Dissimilarity to the \ncentral tendency", facetvar = "Dataset", tails = 1),
-  plot_percentile_hist(all_di, "nsingletons_percentile_mean", "\nProportion of rare species", facetvar = "Dataset"),
-  plot_percentile_hist(all_di, "skew_percentile_mean", "\nSkewness", facetvar = "Dataset", min_s0 = 3),
-  plot_percentile_hist(all_di, "simpson_percentile_mean", "\nSimpson evenness", facetvar = "Dataset"),
-  plot_percentile_hist(all_di, "shannon_percentile_mean", "\nShannon diversity", facetvar = "Dataset")
-), ncol = 3,
-top = textGrob("Figure 3", gp = gpar(fill = "white")), left = textGrob("Number of communities", rot = 90, gp = gpar(fill = "black")),
-bottom = textGrob("Percentile rank of observed value relative to feasible set"), gp = gpar(fill = "white"))
+  plot_percentile_hist(all_di, "real_po_percentile_mean", "Dissimilarity", facetvar = "Dataset", tails = 1),
+  plot_percentile_hist(all_di, "nsingletons_percentile_mean", "Proportion of rare species", facetvar = "Dataset"),
+  plot_percentile_hist(all_di, "skew_percentile_mean", "Skewness", facetvar = "Dataset", min_s0 = 3) + theme(plot.margin = unit(c(1, 2, -5, -5), units = "mm")),
+  plot_percentile_hist(all_di, "simpson_percentile_mean", "Simpson evenness", facetvar = "Dataset"),
+  plot_percentile_hist(all_di, "shannon_percentile_mean", "Shannon diversity", facetvar = "Dataset")
+), ncol = 3, 
+left = textGrob("Number of communities", rot = 90, gp = gpar(fill = "black")),
+bottom = textGrob("Percentile rank of observed value relative to feasible set"), 
+gp = gpar(fill = "white"))
 
-# 
-# 
-# pdf("figure_3.pdf", bg = "white", paper = "letter", width = 8, height = 4)
-# gridExtra::grid.arrange(grobs = list(fig_3), 
-# top = textGrob("Figure 3"))
-# dev.off()
 
 fig_3
 
-ggsave("figure_3.pdf", plot = fig_3, device = "pdf", width = 8, height = 8, units = "in")
+ggsave("figure_3.pdf", plot = fig_3, device = "pdf", width = 180, height = 180, dpi = 800, units = "mm")
 
 ```
 
@@ -366,7 +356,8 @@ plot_narrowness <- function(di_df, yvar, yvar_name) {
     scale_x_log10() +
     ggtitle(yvar_name) +
     theme(legend.position = "none")+
-    theme(plot.title = element_text(size=10))
+    theme(plot.title = element_text(size=10)) +
+    theme(legend.text = element_text(size = 7), plot.margin = unit(c(0, 10, 0, 0), units = "mm"), axis.text = element_text(size = 7))
 }
 
 plot_narrowness_legend <- function(di_df) {
@@ -377,7 +368,7 @@ plot_narrowness_legend <- function(di_df) {
     mutate(ymark = dplyr::row_number())
 
   ggplot(legend_df, aes(1, ymark, color = Dataset)) +
-    geom_label(aes(x = 2, y = ymark, label = Dataset)) +
+    geom_text(aes(x = 2, y = ymark, label = Dataset)) +
     geom_point(size = 4) +
     scale_color_viridis_d(end = .9) +
     xlab("") +
@@ -402,25 +393,32 @@ plot_narrowness_legend <- function(di_df) {
 ```{r f4, fig.dim = c(7,4)}
 
 
+# 
+# fig_4 <- gridExtra::grid.arrange(grobs = list(
+#   plot_narrowness(all_di, "sim_pos_from_best_95", "Dissimilarity \nto central tendency") + ylab("Dissimilarity \n95th percentile") + theme(legend.position = "bottom", legend.direction = "vertical" , legend.margin = margin(b = 40, r = 0, t = 10, l = 0, unit = "mm")),
+#   gridExtra::grid.arrange(grobs = list(
+#     plot_narrowness(all_di, "skew_95_ratio_2t", "\nSkewness"),
+#     plot_narrowness(all_di, "simpson_95_ratio_2t", "\nSimpson evenness")+ ylab(""),
+#     plot_narrowness(all_di, "nsingletons_95_ratio_2t", "\nProportion of rare species"),
+#        plot_narrowness(all_di, "shannon_95_ratio_2t", "\nShannon diversity") + ylab("")
+#   ), ncol = 2)), ncol = 2, widths = c( 2, 4),bottom = textGrob("Number of elements in the feasible set"))
 
 fig_4 <- gridExtra::grid.arrange(grobs = list(
-  plot_narrowness(all_di, "sim_pos_from_best", "Dissimilarity \nto central tendency") + ylab("Mean dissimilarity") + theme(legend.position = "bottom", legend.direction = "vertical" , legend.margin = margin(b = .25, r = 0, t = 0, l = 0, unit = "in")),
-  gridExtra::grid.arrange(grobs = list(
-    plot_narrowness(all_di, "skew_95_ratio_2t", "\nSkewness"),
-    plot_narrowness(all_di, "simpson_95_ratio_2t", "\nSimpson evenness")+ ylab(""),
-    plot_narrowness(all_di, "nsingletons_95_ratio_2t", "\nProportion of rare species"),
-       plot_narrowness(all_di, "shannon_95_ratio_2t", "\nShannon diversity") + ylab("")
-  ), ncol = 2)), ncol = 2, widths = c( 2, 4), bottom = textGrob("Number of elements in the feasible set"), top = textGrob("Figure 4"))
+  plot_narrowness(all_di, "sim_pos_from_best_95", "Dissimilarity") + ylab("Dissimilarity \n95th percentile") + theme(legend.position = c(.65, .8), legend.justification = "center", legend.direction = "horizontal", legend.background = element_blank(), legend.key = element_blank(), legend.key.size = unit(.25, units = "mm"), legend.title = element_text(size =7)),
+    plot_narrowness(all_di, "skew_95_ratio_2t", "Skewness") + ylab("\nBreadth index"),
+    plot_narrowness(all_di, "simpson_95_ratio_2t", "Simpson evenness")+ ylab("\nBreadth index"),
+    plot_narrowness(all_di, "nsingletons_95_ratio_2t", "Proportion of rare species")+ ylab("\nBreadth index"),
+       plot_narrowness(all_di, "shannon_95_ratio_2t", "Shannon diversity")+ ylab("\nBreadth index")), ncol = 1, bottom = textGrob("Number of elements in the feasible set"))
 
 
-fig_4
+#fig_4
 # 
 # pdf("figure_4.pdf", bg = "white", paper = "letter", width = 8, height = 5)
 # fig_4
 # dev.set(dev.next())
 # while (!is.null(dev.list()))  dev.off()
 
-ggsave("figure_4.pdf", plot = fig_4, device = "pdf", width = 8, height = 5, units = "in")
+ggsave("figure_4.pdf", plot = fig_4, device = "pdf", width = 180, height = 180, dpi = 800, units = "mm")
 ```
 
 ```{r}
@@ -517,19 +515,20 @@ nhist <- plot_narrowness_hist(filter(all_di, dat %in% c("fia", "mcdb", "misc_abu
   facet_wrap(vars(`Number of elements`, Dataset), scales = "free_y", nrow = 2, ncol = 3) +
   xlab("Breadth index") +
   ylab("Number of communities") +
-  ggtitle("Skewness")
+  ggtitle("Skewness") + theme(plot.margin = unit(c(5,5,5,5), units = "mm"))
+
 
 phist <- plot_percentile_hist(filter(all_di, dat %in% c("fia", "mcdb", "misc_abund")), "skew_percentile_mean", "Skewness") +
   facet_wrap(vars(`Number of elements`, Dataset), scales = "free_y", nrow = 2, ncol = 3) +
   xlab("Percentile rank of observed value relative to feasible set") +
   ylab("Number of communities") +
-  ggtitle("Skewness")
+  ggtitle("Skewness")+ theme(plot.margin = unit(c(5,5,5,5), units = "mm"))
 
-fig_6 <- gridExtra::grid.arrange(grobs = list(nhist, phist), nrow = 2, top = textGrob("Figure 6"))
+fig_6 <- gridExtra::grid.arrange(grobs = list(nhist, phist), nrow = 2)
 
 fig_6
 
-ggsave("figure_6.pdf", plot = fig_6, device = "pdf", width = 6, height = 8, units = "in")
+ggsave("figure_6.pdf", plot = fig_6, device = "pdf", width = 180, height = 180, dpi = 800, units = "mm")
 
 ```
 
@@ -697,29 +696,38 @@ rs_results_long <- left_join(rs_results_long, metric_names)
 #   scale_color_viridis_d(end = .8) +
 #   ylab("Proportion of extreme observed values") +
 #   xlab("")
+# 
+# fig_5 <- gridExtra::grid.arrange(grobs = list(
+#   ggplot(filter(rs_results_long, !grepl("Misc", Dataset), !weird_dir), aes(metric_desc, value, color = `Resampling scheme`)) +
+#   geom_point() +
+#   facet_wrap(vars(Dataset), scales = "fixed", ncol =2) +
+#   geom_point(aes(y = percentile_cutoff), shape = 95, color = "black", size = 10) +
+#   scale_color_viridis_d(end = .8, option = "plasma") +
+#   ylab("Proportion of extreme observed values") +ylim(0, .7) +
+#   xlab("") + theme(legend.position = "none", axis.text.x = element_text(angle = 90)) ,
+#   ggplot(filter(rs_results_long, grepl("Misc", Dataset), !weird_dir), aes(metric_desc, value, color = `Resampling scheme`)) +
+#   geom_point() +
+#   facet_wrap(vars(Dataset), scales = "fixed", ncol = 2) +
+#   geom_point(aes(y = percentile_cutoff), shape = 95, color = "black", size = 10) +
+#   scale_color_viridis_d(end = .8, option = "plasma") +
+#   ylab("") +
+#   xlab("") + ylim(0, .7) +
+#   theme(legend.position = "bottom", legend.direction = "vertical" , legend.margin = margin(b = .3, r = 0, t = 0, l = 0, unit = "in"), axis.text.x = element_text(angle = 90))), ncol = 2, widths = c( 4,2), bottom = textGrob("Metric"), top = textGrob("Figure 5"))
 
 fig_5 <- gridExtra::grid.arrange(grobs = list(
-  ggplot(filter(rs_results_long, !grepl("Misc", Dataset), !weird_dir), aes(metric_desc, value, color = `Resampling scheme`)) +
+  ggplot(filter(rs_results_long, !weird_dir), aes(metric_desc, value, color = `Resampling scheme`)) +
   geom_point() +
-  facet_wrap(vars(Dataset), scales = "fixed", ncol =2) +
+  facet_wrap(vars(Dataset), scales = "fixed", ncol =5) +
   geom_point(aes(y = percentile_cutoff), shape = 95, color = "black", size = 10) +
-  scale_color_viridis_d(end = .8) +
+  scale_color_viridis_d(end = .8, option = "plasma") +
   ylab("Proportion of extreme observed values") +ylim(0, .7) +
-  xlab("") + theme(legend.position = "none", axis.text.x = element_text(angle = 90)) ,
-  ggplot(filter(rs_results_long, grepl("Misc", Dataset), !weird_dir), aes(metric_desc, value, color = `Resampling scheme`)) +
-  geom_point() +
-  facet_wrap(vars(Dataset), scales = "fixed", ncol = 2) +
-  geom_point(aes(y = percentile_cutoff), shape = 95, color = "black", size = 10) +
-  scale_color_viridis_d(end = .8) +
-  ylab("") +
-  xlab("") + ylim(0, .7) +
-  theme(legend.position = "bottom", legend.direction = "vertical" , legend.margin = margin(b = .3, r = 0, t = 0, l = 0, unit = "in"), axis.text.x = element_text(angle = 90))), ncol = 2, widths = c( 4,2), bottom = textGrob("Metric"), top = textGrob("Figure 5"))
+  xlab("Metric") + theme(legend.position = "bottom", axis.text.x = element_text(angle = 90), plot.margin = unit(c(60, 0, 0, 0), units = "mm"))))
 
-#fig_5
 
 
 
-ggsave("figure_5.pdf", device = "pdf", plot = fig_5, width = 6, height = 5, units = "in")
+ggsave("figure_5.pdf", device = "pdf", plot = fig_5, width = 180, height =
+180, dpi = 800, units = "mm")
 # 
 # pdf("figure_5.pdf", bg = "white", paper = "letter", width = 6, height = 5)
 # fig_5