From 811b8bbbf989f952a688246a453eafe3776abba1 Mon Sep 17 00:00:00 2001
From: unknown <justisnojo@gmail.com>
Date: Thu, 22 Aug 2024 05:35:23 -0700
Subject: [PATCH] fix trait reporting bugs

---
 R/NetworkSim.R       |  4 ++--
 R/sim.bdh.age.help.R | 13 +++++++++----
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/R/NetworkSim.R b/R/NetworkSim.R
index 857d8f8..34f5901 100644
--- a/R/NetworkSim.R
+++ b/R/NetworkSim.R
@@ -384,8 +384,8 @@ handleTipsTaxa<-function(phy,complete,target_ntaxa,current_n){
     phy<-deleteTips(phy,deltips)
     
     if(has_traits){
-      trait_inds<-match(phy$tip.label,old_tip_states) ##how the tips of the new phy mapped to the old one
-      phy$tip.states<-old_tip_states[tip_inds] ##Use the mapping to keep and order the appropriate trait values
+      trait_inds<-match(phy$tip.label,old_tip_names) ##how the tips of the new phy mapped to the old one
+      phy$tip.states<-old_tip_states[trait_inds] ##Use the mapping to keep and order the appropriate trait values
     }
     
   }
diff --git a/R/sim.bdh.age.help.R b/R/sim.bdh.age.help.R
index 8136c32..b329dc4 100644
--- a/R/sim.bdh.age.help.R
+++ b/R/sim.bdh.age.help.R
@@ -408,6 +408,11 @@ sim2.bdh.origin <- function(m=0,n=0,age,lambda,mu,nu,hyb.inher.fxn,hybprops,hyb.
       extinct_tips<-rep(NA,length(extinct)) ##record all extinct tips
       timecreation_order<-rep(NA,length(timecreation)) ##reorder timecreation so node numbers and creation match
       Nextinct<-1
+      
+      if(!is_null_trait){
+        tip_states<-c()
+      }
+      
       for (j in (1:num_nodes)){
         inleaves <- (leaves  %in% (-j))
         inextinct<- (extinct %in% (-j))
@@ -417,14 +422,14 @@ sim2.bdh.origin <- function(m=0,n=0,age,lambda,mu,nu,hyb.inher.fxn,hybprops,hyb.
         } else { ## We are at a tip of some sort (extant,extinct, or hybrid)
           
           if(!is_null_trait){##if a trait model
-            tip_states<-c()
+            
             #record the trait value of the leaf we are at
             
             ##determine if we are at an extant or extinct tip
             if(any(inleaves)){ #we are in an extant leaf
-              trait_value <- trait_states[which(-j==leaves)]
+              trait_value <- trait_state[which(-j==leaves)]
             }else{ ##we are extinct leaf
-              trait_value <- ext_trait_states[which(-j==extinct)]
+              trait_value <- ext_trait_state[which(-j==extinct)]
             }
             tip_states<-c(tip_states,trait_value)
           }
@@ -459,7 +464,7 @@ sim2.bdh.origin <- function(m=0,n=0,age,lambda,mu,nu,hyb.inher.fxn,hybprops,hyb.
       if(!is_null_trait){
         phy$tip.states<-tip_states
       }
-      
+
       if(n!=0){ ##we use these for GSA
         phy$timecreation <- timecreation_order
         if(is.null(time_in_n)){