Add phylogenetic signal as a numeric output in results object

katiesaund · Jul 11, 2020 · 56afa57 · 56afa57
1 parent 430c04b
commit 56afa57
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Showing 3 changed files with 6 additions and 0 deletions.
diff --git a/R/run_continuous.R b/R/run_continuous.R
@@ -111,6 +111,8 @@ run_continuous <- function(args){
   results_object$sig_hits <- corrected_pvals_all_trans$sig_pvals
   results_object$convergence <- convergence
   results_object$non_FDR_hit_pvals <- -log(results_all_transitions$pvals)
+  results_object$phylogenetic_signal <- unname(calculate_lambda(args$phenotype,
+                                                                args$tree))
   save_results_as_r_object(args$output_dir,
                            args$output_name,
                            results_object,

diff --git a/R/run_phyc.R b/R/run_phyc.R
@@ -128,6 +128,8 @@ run_phyc <- function(args){
   results_object$dropped_genotypes <-
     hi_conf$dropped_genotypes
   results_object$convergence <- convergence
+  results_object$phylogenetic_signal <- unname(calculate_d(args$phenotype,
+                                                           args$tree))
   save_results_as_r_object(args$output_dir,
                            args$output_name,
                            results_object,

diff --git a/R/run_synchronous.R b/R/run_synchronous.R
@@ -120,6 +120,8 @@ run_synchronous <- function(args){
     hi_conf$num_high_conf_trans_edges
   results_object$dropped_genotypes <- hi_conf$dropped_genotypes
   results_object$convergence <- convergence
+  results_object$phylogenetic_signal <- unname(calculate_d(args$phenotype,
+                                                           args$tree))
   save_results_as_r_object(args$output_dir,
                            args$output_name,
                            results_object,