From 9d837443fd2260337b560722ab83a7bc6ae0b5ca Mon Sep 17 00:00:00 2001
From: egouldo <egouldo@users.noreply.github.com>
Date: Tue, 3 Sep 2024 00:48:03 +1000
Subject: [PATCH] bug!: update downstream code in
 tbl-deviation-similarity-convergence-singularity-yi #42

---
 supp_mat/SM3_ExplainingDeviation.qmd | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/supp_mat/SM3_ExplainingDeviation.qmd b/supp_mat/SM3_ExplainingDeviation.qmd
index bf874b8..f5643d2 100644
--- a/supp_mat/SM3_ExplainingDeviation.qmd
+++ b/supp_mat/SM3_ExplainingDeviation.qmd
@@ -1054,10 +1054,8 @@ patchwork::wrap_plots(yi_sorensen_plots,heights = 4, byrow = TRUE) +
 #| message: false
 
 yi_singularity_convergence_sorensen_mixed_mod %>% 
-  filter(dataset != "blue tit" | str_detect(model_name, 
-                                            "random", 
-                                            negate = TRUE)) %>% 
-  select(-params) %>% 
+  select(-model_params) %>% 
+  group_by(model_name) %>% 
   gt::gt(rowname_col = "dataset") %>% 
   gt::tab_style(locations = cells_body(rows = str_detect(dataset, "Eucalyptus"),
                                        columns = dataset),
@@ -1065,21 +1063,24 @@ yi_singularity_convergence_sorensen_mixed_mod %>%
   gt::cols_label(dataset = "Dataset",
                  estimate_type = "Estimate Type",
                  singularity = "Singular Fit?",
-                 convergence = "Model converged?") %>% 
+                 convergence = "Model converged?",
+                 SE_calc = "Can random effects SE be calculated?",
+                 CI_calc = "Can random effects CI be calculated?") %>% 
   gt::opt_stylize(style = 6, color = "gray") %>% 
-  tab_style(
+   tab_style(
     style = list(
       cell_fill(color = scales::alpha("red", 0.6)),
       cell_text(color = "white", weight = "bold")
     ),
     locations = list(
       cells_body(columns = "singularity", rows = singularity == TRUE),
-      cells_body(columns = "convergence", rows = convergence == FALSE)
-    )
-  )  %>% 
+      cells_body(columns = "convergence", rows = convergence == FALSE),
+      cells_body(columns = "SE_calc", rows = SE_calc == FALSE),
+      cells_body(columns = "CI_calc", rows = CI_calc == FALSE)
+    )) %>% 
   gt::text_transform(fn = function(x) ifelse(x == TRUE, "yes", "no" ),
                      locations = cells_body(columns = c("singularity",
-                                                        "convergence")
+                                                        "convergence", "SE_calc", "CI_calc")
                      )) %>% 
   gt::text_transform(
     locations = cells_stub(