EnquistLab · TanyaS08 · May 17, 2021 · May 17, 2021 · May 17, 2021 · May 17, 2021
diff --git a/figures/Figure_1.png b/figures/Figure_1.png
diff --git a/figures/Figure_2.png b/figures/Figure_2.png
diff --git a/figures/Figure_3.png b/figures/Figure_3.png
diff --git a/figures/Figure_4.png b/figures/Figure_4.png
diff --git a/figures/Figure_5.png b/figures/Figure_5.png
diff --git a/figures/Figure_SI_1.png b/figures/Figure_SI_1.png
diff --git a/figures/Figure_SI_10.png b/figures/Figure_SI_10.png
diff --git a/figures/Figure_SI_11.png b/figures/Figure_SI_11.png
diff --git a/figures/Figure_SI_12.png b/figures/Figure_SI_12.png
diff --git a/figures/Figure_SI_2.png b/figures/Figure_SI_2.png
diff --git a/figures/Figure_SI_3.png b/figures/Figure_SI_3.png
diff --git a/figures/Figure_SI_4.png b/figures/Figure_SI_4.png
diff --git a/figures/Figure_SI_5.png b/figures/Figure_SI_5.png
diff --git a/figures/Figure_SI_6.png b/figures/Figure_SI_6.png
diff --git a/figures/Figure_SI_7.png b/figures/Figure_SI_7.png
diff --git a/figures/Figure_SI_8.png b/figures/Figure_SI_8.png
diff --git a/figures/Figure_SI_9.png b/figures/Figure_SI_9.png
diff --git a/figures/Figures.zip b/figures/Figures.zip
diff --git a/figures/pdf/Figure_2.pdf b/figures/pdf/Figure_2.pdf
diff --git a/figures/pdf/Figure_3.pdf b/figures/pdf/Figure_3.pdf
diff --git a/figures/pdf/Figure_4.pdf b/figures/pdf/Figure_4.pdf
diff --git a/figures/pdf/Figure_5.pdf b/figures/pdf/Figure_5.pdf
diff --git a/figures/pdf/Figure_SI_1.pdf b/figures/pdf/Figure_SI_1.pdf
diff --git a/figures/pdf/Figure_SI_10.pdf b/figures/pdf/Figure_SI_10.pdf
diff --git a/figures/pdf/Figure_SI_11.pdf b/figures/pdf/Figure_SI_11.pdf
diff --git a/figures/pdf/Figure_SI_12.pdf b/figures/pdf/Figure_SI_12.pdf
diff --git a/figures/pdf/Figure_SI_2.pdf b/figures/pdf/Figure_SI_2.pdf
diff --git a/figures/pdf/Figure_SI_3.pdf b/figures/pdf/Figure_SI_3.pdf
diff --git a/figures/pdf/Figure_SI_4.pdf b/figures/pdf/Figure_SI_4.pdf
diff --git a/figures/pdf/Figure_SI_5.pdf b/figures/pdf/Figure_SI_5.pdf
diff --git a/figures/pdf/Figure_SI_6.pdf b/figures/pdf/Figure_SI_6.pdf
diff --git a/figures/pdf/Figure_SI_7.pdf b/figures/pdf/Figure_SI_7.pdf
diff --git a/figures/pdf/Figure_SI_8.pdf b/figures/pdf/Figure_SI_8.pdf
diff --git a/figures/pdf/Figure_SI_9.pdf b/figures/pdf/Figure_SI_9.pdf
diff --git a/images/moons_legend_light.png b/images/moons_legend_light.png
diff --git a/images/traitstrap_hex.png b/images/traitstrap_hex.png
diff --git a/r_functions/tidy_simdata.R b/r_functions/tidy_simdata.R
@@ -28,15 +28,15 @@ tidy_simdata <-function(data){
                               TRUE ~ moment),
            method = case_when(method == 'global cwm' ~ 'Cross-Site CW',
                               method == 'site-specic CWM' ~ 'Site-Specific CW',
-                              method == 'nonparametric bs' ~ 'Non-Parametric BS',
+                              method == 'nonparametric bs' ~ 'Nonparametric BS',
                               method == 'parametric bs' ~ 'Parametric BS',
                               TRUE ~ method)) %>%
     filter(true_moment == moment) %>%
     select(-c(global, true_moment, ci_low_moment, ci_high_moment)) %>%
     mutate(method = ordered(method,levels = c("Cross-Site CW",
                                               "Site-Specific CW",
                                               "Parametric BS",
-                                              "Non-Parametric BS")),
+                                              "Nonparametric BS")),
            overunder = ifelse(true_value <= estimate,
                               "over",
                               "under"),

diff --git a/scripts_for_ms_with_traitstrap/2_simulation_analyses_and_figures.R b/scripts_for_ms_with_traitstrap/2_simulation_analyses_and_figures.R
@@ -62,7 +62,7 @@ cowplot::ggdraw(
                    y = method,
                    fill = method,
                    alpha = hit),
-               color = colorspace::lighten("#5e5e5e", 0.3),
+               color = colorspace::lighten("grey69", 0.3),
                size = 1, stroke = 0.2,
                position = position_jitternormal(sd_x = 0, sd_y = 0.1), 
                shape = 21) +
@@ -811,8 +811,8 @@ lollipop_CO =
                                           angle = 0),
          strip.text.x.top = element_text(size = rel(1.3)),
          legend.position = 'top',
-         legend.background = element_rect(colour = colorspace::darken("#dddddd", 0.1),
-                                          size = 0.4),
+         # legend.background = element_rect(colour = colorspace::darken("#dddddd", 0.1),
+         #                                  size = 0.4),
          legend.margin = margin(3, 5, 3, 5),
          plot.margin = margin(5, 0, 7, 0))
  +
@@ -882,8 +882,9 @@ lollipop_CO =
                 align_to = 'full', 
                 ignore_tag = TRUE) + theme_void()  +
   plot_annotation(theme = theme(
-                    plot.background = element_rect(fill = "white", colour = NA),
-                    panel.background = element_rect(fill = "white", colour = NA),
+                    plot.background = element_rect(fill = "#141438", colour = NA),
+                    panel.background = element_rect(fill = "#141438", colour = NA),
+                    legend.background = element_rect(fill = "#141438", colour = NA),
                     text = element_text(face = 'bold'))) +
   plot_layout(heights = c(1, 0.15, 0.15))
 
@@ -1069,3 +1070,4 @@ ggsave(here::here("figures/Figure_SI_5.png"),
 ggsave(here::here("figures/pdf/Figure_SI_5.pdf"),
        height = 314, width = 180,
        units = "mm", dpi = 600)
+
diff --git a/scripts_for_ms_with_traitstrap/3_distrubution_figure.R b/scripts_for_ms_with_traitstrap/3_distrubution_figure.R
@@ -125,7 +125,7 @@ np_dist <- get_distributions(imputed_traits = imputed_full,nrep = n_distribution
 
 
 
-np_dist$method <- "Non-parametric BS"
+np_dist$method <- "Nonparametric BS"
 pbs_dist$method <- "Parametric BS"
 cwm_dist$method <- "Cross-Site WM"
 cwm_site_dist$method <- "Site-Specific WM"
@@ -151,7 +151,7 @@ rm(atraits_dist)
 all_dists$method <- factor(all_dists$method,
                            levels = c("Cross-Site WM",
                                       "Site-Specific WM",
-                                      "Non-parametric BS",
+                                      "Nonparametric BS",
                                       "Parametric BS",
                                       "True"))
 
@@ -167,7 +167,7 @@ joy_plot =
   scale_colour_manual(guide = guide_legend(title = "Method",
                                            title.position="top",
                                            title.hjust = 0.5),
-                      values = c(pal_df$c, "#5e5e5e"),
+                      values = c(pal_df$c, "grey69"),
                       labels = c(pal_df$l, "True")) +
   guides(colour = guide_legend(override.aes = list(linetype = c(1, 1, 1, 1, 3)),
                                title = "Method",
@@ -216,14 +216,14 @@ joy_plot =
   guides(alpha = 'none')  +
   figure_theme +
   theme(axis.text.x = element_blank(),
-        panel.background = element_rect(colour = '#5e5e5e',
+        panel.background = element_rect(colour = "grey69",
                                         size = 0.3),
         strip.text.y = element_text(margin = margin(0, 0, 10, 0),
                                     size = rel(.9), face = "bold",
-                                    colour = "#5e5e5e"),
+                                    colour = "grey69"),
         strip.text.x.top = element_text(margin = margin(0, 0, 10, 0),
                                         size = rel(.9), face = "bold",
-                                        colour = "#5e5e5e"),
+                                        colour = "grey69"),
         strip.background = element_blank(),
         axis.line = element_blank(),
         strip.placement = 'outside',
@@ -263,7 +263,7 @@ ggsave(here::here("figures/pdf/Figure_SI_1.pdf"),
 
 np_dist_3x <- get_distributions(imputed_traits = imputed_full,nrep = 3,sample_size = sample_size_dist)
 np_dist_3x <- merge(np_dist_3x,elev)
-np_dist_3x$method <- "Non-parametric BS"
+np_dist_3x$method <- "Nonparametric BS"
 np_dist_3x$n <- paste("Replicate",np_dist_3x$n)
 
 atraits_dist <- atraits

diff --git a/scripts_for_ms_with_traitstrap/4_biased_simulation_analyses_and_figures.R b/scripts_for_ms_with_traitstrap/4_biased_simulation_analyses_and_figures.R
@@ -385,29 +385,32 @@ inset_AZ <-
 colorado_percent <- readRDS("output_data/Colorado_percent_community_sims.RDS")
 
 colorado_percent$method = fct_recode(colorado_percent$method, `Cross-Site CW` = "Cross-Site CWM", 
-                                     `Site-Specific CW` = "Site-Specific CWM")
+                                     `Site-Specific CW` = "Site-Specific CWM",
+                                     `Nonparametric BS` = 'Non-Parametric BS')
 
 panama_percent <- readRDS("output_data/Panama_percent_community_sims.RDS")
 
 panama_percent$method = fct_recode(panama_percent$method, `Cross-Site CW` = "Cross-Site CWM", 
-                                   `Site-Specific CW` = "Site-Specific CWM")
+                                   `Site-Specific CW` = "Site-Specific CWM",
+                                   `Nonparametric BS` = 'Non-Parametric BS')
 
 rodent_percent <- readRDS("output_data/Rodent_percent_community_sims.RDS")
 
 rodent_percent$method = fct_recode(rodent_percent$method, `Cross-Site CW` = "Cross-Site CWM", 
-                                   `Site-Specific CW` = "Site-Specific CWM")
+                                   `Site-Specific CW` = "Site-Specific CWM",
+                                   `Nonparametric BS` = 'Non-Parametric BS')
 
 
 rodent_percent$method <- ordered(rodent_percent$method,
                                  levels = c("Cross-Site CW",
                                             "Site-Specific CW",
                                             "Parametric BS",
-                                            "Non-Parametric BS"))
+                                            "Nonparametric BS"))
 
 colorado_percent$method <- ordered(colorado_percent$method,
-                                   levels = c("Cross-Site CW","Site-Specific CW","Parametric BS","Non-Parametric BS"))
+                                   levels = c("Cross-Site CW","Site-Specific CW","Parametric BS","Nonparametric BS"))
 panama_percent$method <- ordered(panama_percent$method,
-                                 levels = c("Cross-Site CW","Site-Specific CW","Parametric BS","Non-Parametric BS"))
+                                 levels = c("Cross-Site CW","Site-Specific CW","Parametric BS","Nonparametric BS"))
 
 colorado_percent$moment =
   ordered(colorado_percent$moment,levels = c("mean",
@@ -421,6 +424,7 @@ rodent_percent$moment =
                                            "skewness",
                                            "kurtosis"))
 
+
 #### Combine CO and AZ ----
 
 data <- vector('list', 2)
@@ -675,7 +679,7 @@ CC
               # heights = c(1, 0.7),
               design = layout) +
   plot_annotation(theme = theme(
-    plot.background = element_rect(fill = "white", colour = NA),
+    plot.background = element_rect(fill = "#141438", colour = NA),
     legend.position = 'right')) +
   inset_element(moon_legend,
                 left = 0.87,
@@ -846,8 +850,8 @@ for (i in 1:5) {
                    align_to = 'full') + theme_void()) +
   plot_layout(guides = 'collect') +
   plot_annotation(theme = theme(
-    plot.background = element_rect(fill = "white", colour = NA),
-    panel.background = element_rect(fill = "white", colour = NA),
+    plot.background = element_rect(fill = "#141438", colour = NA),
+    panel.background = element_rect(fill = "#141438", colour = NA),
     legend.position = 'bottom')) 
 
 ggsave(here::here("figures/Figure_SI_7.png"),

diff --git a/scripts_for_ms_with_traitstrap/5_plankton_timeseries.R b/scripts_for_ms_with_traitstrap/5_plankton_timeseries.R
@@ -35,7 +35,7 @@ cowplot::ggdraw(
                   y = true_value,
                   group = method,
                   linetype = "True value"),
-              colour = 'grey30',
+              colour = 'grey69',
               size = 0.4, smooth = 3) +
     geom_ribbon(aes(
       x = as.numeric(site),
@@ -68,7 +68,7 @@ cowplot::ggdraw(
                                                title.position="top",
                                                title.hjust = 0.5,
                                                override.aes = 
-                                                 list(colour = c("grey69","grey30")))) +
+                                                 list(colour = c("grey90","grey69")))) +
     facet_grid(rows = vars(moment),
                cols = vars(method),
                labeller = labeller(

diff --git a/scripts_for_ms_with_traitstrap/6_comparing_CWM_methods.R b/scripts_for_ms_with_traitstrap/6_comparing_CWM_methods.R
@@ -66,7 +66,7 @@ cowplot::ggdraw(
     geom_abline(aes(slope = 1, 
                     intercept = 0,
                     linetype = "1:1 line"),
-                colour = "black") +
+                colour = "white") +
     geom_ribbon(data = cwm_CI,
                 aes(x = traditional_CWM,
                     ymin = ci_low,
@@ -76,7 +76,7 @@ cowplot::ggdraw(
                 aes(slope = grad, 
                     intercept = yint,
                     linetype = "Regression slope"),
-                colour = "grey69",
+                colour = "grey60",
                 alpha = 0.9) +
     geom_point(aes(x = traditional_CWM,
                    y = bootstrap_CWM),
@@ -87,7 +87,7 @@ cowplot::ggdraw(
                alpha = 0.5) +
     geom_point(aes(x = traditional_CWM,
                    y = bootstrap_CWM),
-               colour = "grey69",
+               colour = "grey60",
                fill = NA,
                shape = 21,
                size = 2,
@@ -121,7 +121,7 @@ cowplot::ggdraw(
     scale_linetype_manual("",
                           values=c("1:1 line" = 2,
                                    "Regression slope" = 1),
-                          guide = guide_legend(override.aes = list(colour = c("black","grey69")))) +
+                          guide = guide_legend(override.aes = list(colour = c("white","grey60")))) +
     coord_cartesian(clip = "off") +
     theme_moon +
     theme(axis.ticks.length=unit(.5, "mm"),
@@ -222,18 +222,18 @@ for (i in 1:length(samp_size)) {
     # Theme
     figure_theme +
     theme(
-      axis.text = element_text(color = "#5e5e5e", size = rel(.4)),
-      axis.title = element_text(color = "#5e5e5e", size = rel(.5)),
-      legend.text = element_text(color = "#5e5e5e", size = rel(.5)),
-      legend.title = element_text(color = "#5e5e5e", size = rel(.6)),
+      axis.text = element_text(color = "grey69", size = rel(.4)),
+      axis.title = element_text(color = "grey69", size = rel(.5)),
+      legend.text = element_text(color = "grey69", size = rel(.5)),
+      legend.title = element_text(color = "grey69", size = rel(.6)),
       strip.text.y = element_text(margin = margin(0, 0, 3, 0),
                                   size = rel(.6), face = "bold",
-                                  color = "#5e5e5e"),
+                                  color = "grey69"),
       strip.text.x.top = element_text(margin = margin(0, 0, 3, 0),
                                       size = rel(.6),
-                                      color = "#5e5e5e", face = "bold"),
+                                      color = "grey69", face = "bold"),
       panel.grid.major.y = element_line(size = 0.03,
-                                        color = "#5e5e5e"),
+                                        color = "grey69"),
       strip.background = element_blank(),
       axis.line = element_blank(),
       strip.placement = 'outside',
@@ -242,7 +242,7 @@ for (i in 1:length(samp_size)) {
       plot.title.position = "panel",
       plot.title = element_text(margin = margin(0, 0, 10, 0),
                                 size = rel(.5), face = "bold",
-                                color = "#5e5e5e"),
+                                color = "grey69"),
       legend.position = 'bottom',
       plot.margin = margin(2, 2, 2, 2),
       legend.key.size = unit(3, "mm"),
@@ -272,8 +272,8 @@ for (i in 1:length(samp_size)) {
      labs(title = "F: Bootstrap sample size: 1 600")) +
   plot_layout(guides = 'collect') +
   plot_annotation(theme = theme(
-                    plot.background = element_rect(fill = "white", colour = NA),
-                    panel.background = element_rect(fill = "white", colour = NA),
+                    plot.background = element_rect(fill = "#141438", colour = NA),
+                    panel.background = element_rect(fill = "#141438", colour = NA),
                     legend.position = 'none')
   ) 
 
@@ -305,7 +305,7 @@ ggplot(bs_ci) +
   geom_line(aes(x = boot_sample_size,
                 y = true_value,
                 linetype = "True value"),
-            colour = 'grey30',
+            colour = 'grey90',
             size = 0.5) +
   geom_bump(aes(x = boot_sample_size,
                 y = estimate,
@@ -324,7 +324,7 @@ ggplot(bs_ci) +
                                              title.position="top",
                                              title.hjust = 0.5,
                                              override.aes = 
-                                               list(colour = c("grey69","grey30")))) +
+                                               list(colour = c("grey69","grey90")))) +
   scale_colour_manual(guide = guide_legend(title = "Method",
                                            title.position="top",
                                            title.hjust = 0.5),

diff --git a/scripts_for_ms_with_traitstrap/7_global_mean.R b/scripts_for_ms_with_traitstrap/7_global_mean.R
@@ -27,7 +27,7 @@ global =
                             TRUE ~ moment),
          method = case_when(method == 'global cwm' ~ 'Cross-Site CW',
                             method == 'site-specic CWM' ~ 'Site-Specific CW',
-                            method == 'nonparametric bs' ~ 'Non-Parametric BS',
+                            method == 'nonparametric bs' ~ 'Nonparametric BS',
                             method == 'parametric bs' ~ 'Parametric BS',
                             TRUE ~ method)) %>%
   pivot_longer(cols = contains('true'),
@@ -40,7 +40,7 @@ global =
   mutate(method = ordered(method,levels = c("Cross-Site CW",
                                             "Site-Specific CW",
                                             "Parametric BS",
-                                            "Non-Parametric BS"))) %>%
+                                            "Nonparametric BS"))) %>%
   left_join(.,
             readRDS("data/elevations.RDS")) %>%
   distinct(trait_source, method, site, trait, moment, n, estimate,
@@ -50,7 +50,7 @@ global =
                                             "skewness",
                                             "kurtosis"))) %>%
   filter(method %in% c("Cross-Site CW",
-                       "Non-Parametric BS"))
+                       "Nonparametric BS"))
 
 
 
@@ -67,7 +67,7 @@ for (i in 1:length(trait_select)) {
     geom_line(aes(x = mean_elev,
                   y = true_value,
                   linetype = "True value"),
-              colour = "grey30",
+              colour = "grey69",
               size = 0.8) +
     geom_ribbon(data = global %>%
                   filter(trait == trait_select[i]) %>%
@@ -115,9 +115,9 @@ for (i in 1:length(trait_select)) {
                           guide = guide_legend(title = "Data source",
                                                title.position="top",
                                                title.hjust = 0.5,
-                                               override.aes = list(colour = c("grey69",
-                                                                              "grey69",
-                                                                              "grey30"),
+                                               override.aes = list(colour = c("grey90",
+                                                                              "grey90",
+                                                                              "grey69"),
                                                                    size = 0.5))) +
     labs(x = "Elevation (m)",
          y = "Estimate") +
@@ -151,8 +151,8 @@ global_plots[[1]] +
         strip.text.y = element_blank()) +
   plot_layout(guides = 'collect') +
   plot_annotation(theme = theme(
-    plot.background = element_rect(fill = "white", colour = NA),
-    panel.background = element_rect(fill = "white", colour = NA),
+    plot.background = element_rect(fill = "#141438", colour = NA),
+    panel.background = element_rect(fill = "#141438", colour = NA),
     legend.position = 'bottom'))
 
 ggsave(here::here("figures/Figure_4.png"),