Implementing changes from issue #86 and issue #89

PoonLab · Jul 17, 2017 · b8f1f39 · b8f1f39
1 parent 9312663
commit b8f1f39
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diff --git a/pkg/R/compartmental-models.R b/pkg/R/compartmental-models.R
@@ -45,8 +45,15 @@ require(rcolgem, quietly=TRUE)
     integrationMethod=integrationMethod  #  , n.reps=nreps   --this isn't a parameter in rcolgem's simulate.binary.dated.tree.fgy
   )
 
+  # strip out unnecessary attributes from rcolgem returned object
+  phy <- list(
+    edge=tree$edge,
+    Nnode=tree$Nnode,
+    tip.label=tree$tip.label,
+    edge.length=tree$edge.length
+  )
   class(tree)  <- 'phylo'
-  return(tree)            # returning an ape phylo object + 20 other things (from rcolgem)
+  return(tree)            # returning an ape phylo object
 }
 
 

diff --git a/pkg/R/smcConfig.R b/pkg/R/smcConfig.R
@@ -259,6 +259,7 @@ plot.smc.config <- function(config, nreps=1000, numr=1, numc=1) {
       } 
     }
   }
+  par(ask=F)
 }
 
 # parse tip arguments for each model and creates either n tips of zero height if arg is an int