update time_tree

geoepi · Aug 10, 2024 · d1ec77d · d1ec77d
1 parent 10bdad3
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Showing 10 changed files with 67 additions and 53 deletions.
diff --git a/R/plot_time_tree.R b/R/plot_time_tree.R
@@ -49,7 +49,7 @@ plot_time_tree <- function(tree, stats, legend_pos = c(0.3, 0.7)) {
         legend.key.width = unit(3,"line"),
         legend.text = element_text(size=20, face="bold"),
         legend.title = element_text(size=25, face="bold"), 
-        plot.margin = unit(c(1,8,1,1), "mm"))
+        plot.margin = unit(c(1,8,1,0.1), "mm"))
 
   return(p)
 }
diff --git a/docs/search.json b/docs/search.json
diff --git a/docs/site_libs/bootstrap/bootstrap.min.css b/docs/site_libs/bootstrap/bootstrap.min.css
diff --git a/docs/time_tree.html b/docs/time_tree.html
diff --git a/docs/time_tree_files/figure-html/unnamed-chunk-10-1.png b/docs/time_tree_files/figure-html/unnamed-chunk-10-1.png
diff --git a/docs/time_tree_files/figure-html/unnamed-chunk-4-1.png b/docs/time_tree_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/time_tree_files/figure-html/unnamed-chunk-5-1.png b/docs/time_tree_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/time_tree_files/figure-html/unnamed-chunk-7-1.png b/docs/time_tree_files/figure-html/unnamed-chunk-7-1.png
diff --git a/docs/time_tree_files/figure-html/unnamed-chunk-8-1.png b/docs/time_tree_files/figure-html/unnamed-chunk-8-1.png
diff --git a/time_tree.qmd b/time_tree.qmd
@@ -68,10 +68,8 @@ source_dir(here("R"))
 
 ```
 
-## Time Calibrated Phylogenies
 
-
-### Serotype A   
+## Serotype A   
 Check tree model statistics the *get_tracer_stats()* function calculates similar summary statistics as the Tracer software typically used with BEAST.  
 ```{r message=FALSE, warning=FALSE}
 check_stats <- get_tracer_stats(here("local/beast/a_1/As_rev.log"))
@@ -109,11 +107,11 @@ plot_time_tree(sero_A.tree, check_stats)
 FMDV Effective Population Size    
 Trees were run using several different clock and prior choices, all showed flat-line Ne.  The one here was the simplest, coalescent with contant population size.    
 ```{r fig.width=8, fig.height=6, warning=FALSE, message=FALSE}
-phylodynamic_process(sero_A.tree, check_stats, x_limits = c("2009-01-01", "2017-01-01"))
+phylodynamic_process(sero_A.tree, check_stats, x_limits = c("2011-01-01", "2013-01-01"))
 ```
 
 
-### Serotype Asia1   
+## Serotype Asia1   
 ```{r}
 check_stats <- get_tracer_stats(here("local/beast/asia1_1/Asia1s.log"))
 
@@ -152,7 +150,7 @@ Flat Ne, like the other serotypes
 phylodynamic_process(sero_Asia1.tree, check_stats, x_limits = c("2011-01-01", "2013-01-01"))
 ```
 
-### Serotype O   
+## Serotype O   
 ```{r}
 check_stats <- get_tracer_stats(here("local/beast/o_1/sero_0.log"))