update resolveTreeChar example code

Author: dwbapst

R/resolveTreeChar.R

@@ -95,18 +95,22 @@
 #' 
 #' # examples with simulated data
 #' 
-#' set.seed(2)
+#' set.seed(44)   #2
 #' tree <- rtree(50)
 #' #simulate under a likelihood model
-#' trait <- rTraitDisc(tree,k = 3,rate = 0.7)
-#' tree <- degradeTree(tree,prop_collapse = 0.6)
-#' tree <- ladderize(tree,right = FALSE)
+#' trait <- rTraitDisc(tree, k = 3, rate = 0.7)
+#' tree <- degradeTree(tree, prop_collapse = 0.6)
+#' tree <- ladderize(tree, right = FALSE)
 #' 
 #' #a bunch of type = MPR (default) examples
-#' treeUnord <- resolveTreeChar(tree,trait,orderedChar = FALSE)
-#' treeOrd <- resolveTreeChar(tree,trait,orderedChar = TRUE,stateBias = NULL)
-#' treeOrdPrim <- resolveTreeChar(tree,trait,orderedChar = TRUE,stateBias = "primitive")
-#' treeOrdDer <- resolveTreeChar(tree,trait,orderedChar = TRUE,stateBias = "derived")
+#' treeUnord <- resolveTreeChar(tree, trait, 
+#'     orderedChar = FALSE)
+#' treeOrd <- resolveTreeChar(tree, trait, 
+#'     orderedChar = TRUE, stateBias = NULL)
+#' treeOrdPrim <- resolveTreeChar(tree, trait, 
+#'     orderedChar = TRUE, stateBias = "primitive")
+#' treeOrdDer <- resolveTreeChar(tree, trait, 
+#'     orderedChar = TRUE, stateBias = "derived")
 #' 
 #' #compare number of nodes
 #' Nnode(tree)			#original
@@ -117,38 +121,49 @@
 #' 
 #' #let's compare original tree with unordered-resolved tree
 #' layout(1:2)
-#' quickAncPlot(tree,trait,orderedChar = FALSE,cex = 0.3)
-#' text(x = 43,y = 10,"Original",cex = 1.5)
-#' quickAncPlot(treeUnord,trait,orderedChar = FALSE,cex = 0.3)
-#' text(x = 43,y = 10,"orderedChar = FALSE",cex = 1.5)
+#' quickAncPlot(tree, trait, 
+#'     orderedChar = FALSE, cex = 0.3)
+#' text(x = 43, y = 10,"Original", cex = 1.5)
+#' quickAncPlot(treeUnord, trait, 
+#'     orderedChar = FALSE, cex = 0.3)
+#' text(x = 43, y = 10, "orderedChar = FALSE", cex = 1.5)
 #' #some resolution gained
 #' 
 #' #now let's compare the original and ordered, both biasStates = NULL
 #' layout(1:2)
-#' quickAncPlot(tree,trait,orderedChar = FALSE,cex = 0.3)
+#' quickAncPlot(tree, trait, 
+#'     orderedChar = FALSE,cex = 0.3)
 #' text(x = 43,y = 10,"Original",cex = 1.5)
-#' quickAncPlot(treeOrd,trait,orderedChar = TRUE,cex = 0.3)
+#' quickAncPlot(treeOrd, trait, 
+#'     orderedChar = TRUE,cex = 0.3)
 #' text(x = 43,y = 10,"orderedChar = TRUE",cex = 1.5)
 #' 
 #' #now let's compare the three ordered trees
 #' layout(1:3)
-#' quickAncPlot(treeOrd,trait,orderedChar = TRUE,cex = 0.3)
-#' text(x = 41,y = 8,"ordered, biasStates = NULL",cex = 1.5)
-#' quickAncPlot(treeOrdPrim,trait,orderedChar = TRUE,cex = 0.3)
-#' text(x = 41.5,y = 8,"ordered, biasStates = 'primitive'",cex = 1.5)
-#' quickAncPlot(treeOrdDer,trait,orderedChar = TRUE,cex = 0.3)
+#' quickAncPlot(treeOrd, trait, 
+#'     orderedChar = TRUE,cex = 0.3)
+#' text(x = 41, y = 8, 
+#'     "ordered, biasStates = NULL", cex = 1.5)
+#' quickAncPlot(treeOrdPrim, trait, 
+#'     orderedChar = TRUE,cex = 0.3)
+#' text(x = 41.5, y = 8, 
+#'     "ordered, biasStates = 'primitive'", cex = 1.5)
+#' quickAncPlot(treeOrdDer, trait, 
+#'     orderedChar = TRUE,cex = 0.3)
 #' text(x = 42,y = 8,"ordered, biasStates = 'derived'",cex = 1.5)
 #' 
 #' #let's compare unordered with ordered, biasStates = 'primitive'
 #' layout(1:2)
-#' quickAncPlot(treeUnord,trait,orderedChar = FALSE,cex = 0.3)
-#' text(x = 41,y = 8,"orderedChar = FALSE",cex = 1.5)
-#' quickAncPlot(treeOrdPrim,trait,orderedChar = TRUE,cex = 0.3)
-#' text(x = 40,y = 11,"orderedChar = TRUE",cex = 1.5)
-#' text(x = 40,y = 4,"biasStates = 'primitive'",cex = 1.5)
+#' quickAncPlot(treeUnord, trait, 
+#'     orderedChar = FALSE, cex = 0.3)
+#' text(x = 41, y = 8, "orderedChar = FALSE", cex = 1.5)
+#' quickAncPlot(treeOrdPrim, trait, 
+#'     orderedChar = TRUE, cex = 0.3)
+#' text(x = 40, y = 11, "orderedChar = TRUE", cex = 1.5)
+#' text(x = 40, y = 4, "biasStates = 'primitive'", cex = 1.5)
 #' 
 #' 
-#' #these comparisons will differ greatly between datasets
+#' #these comparisons will differ greatly between data sets
 #' 	# need to try them on your own
 #' 
 #' layout(1)