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allow ... to pass to fitMk

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liamrevell committed Sep 21, 2016
1 parent 0a029f9 commit 4b1465ff0fdddf1112060163bfa9194382bb2c8a
Showing with 3 additions and 3 deletions.
  1. +3 −3 R/make.simmap.R
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@@ -49,7 +49,7 @@ make.simmap<-function(tree,x,model="SYM",nsim=1,...){
root<-N+1
# get conditional likelihoods & model
if(is.character(Q)&&Q=="empirical"){
XX<-getPars(bt,xx,model,Q=NULL,tree,tol,m,pi=pi)
XX<-getPars(bt,xx,model,Q=NULL,tree,tol,m,pi=pi,...)
L<-XX$L
Q<-XX$Q
logL<-XX$loglik
@@ -191,8 +191,8 @@ mcmcQ<-function(bt,xx,model,tree,tol,m,burnin,samplefreq,nsim,vQ,prior){
# get pars
# written by Liam J. Revell 2013
getPars<-function(bt,xx,model,Q,tree,tol,m,liks=TRUE,pi){
obj<-fitMk(bt,xx,model,fixedQ=Q,output.liks=liks,pi=pi)
getPars<-function(bt,xx,model,Q,tree,tol,m,liks=TRUE,pi,...){
obj<-fitMk(bt,xx,model,fixedQ=Q,output.liks=liks,pi=pi,...)
N<-length(bt$tip.label)
II<-obj$index.matrix+1
lvls<-obj$states

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