fix trait reporting bugs

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
     }
 
   }

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)){