better plot example; binary data storage

DESCRIPTION

@@ -2,7 +2,7 @@ Package: ouch
 Type: Package
 Title: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
 Version: 2.16-7
-Date: 2021-05-09
+Date: 2021-05-10
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]"),
 	  person(given=c("Marguerite","A."),family="Butler",role=c("ctb")))
 Maintainer: Aaron A. King <[email protected]>

R/plot.R

@@ -155,6 +155,7 @@ arrange_tree <- function (root, anc, cs, ypos = numeric(length(anc))) {
 #' @importFrom graphics par
 #' @importFrom grDevices rainbow
 #' @importFrom stats setNames
+#' @example examples/bimac2.R
 #' @export
 setMethod(
   "plot",

examples/bimac1.R

@@ -6,15 +6,3 @@ tree
 
 plot(tree)
 plot(tree, node.names=TRUE)    # display node names
-
-## When taxon names are long, they are cut off when the
-## default settings are used.  For example:
-tree2 <- with(
-  bimac,
-  ouchtree(nodes=node,ancestors=ancestor,times=time,
-    labels=ifelse(is.na(species),NA,paste(species,island,sep=", "))
-  )
-)
-plot(tree2) # long species names are cut off
-## This is fixed by increasing right margin and font size:
-plot(tree2,margin=0.5)

examples/bimac2.R

@@ -0,0 +1,20 @@
+tree <- with(
+  bimac,
+  ouchtree(nodes=node,ancestors=ancestor,times=time,labels=spcode)
+)
+
+plot(tree)
+plot(tree, node.names=TRUE)    # display node names
+
+## When taxon names are long, they are cut off when the
+## default settings are used.  For example:
+tree2 <- with(
+  bimac,
+  ouchtree(nodes=node,ancestors=ancestor,times=time,
+    labels=ifelse(is.na(species),NA,paste(species,island,sep=", "))
+  )
+)
+
+plot(tree2) # long species names are cut off
+## This is fixed by increasing right margin and font size:
+plot(tree2,margin=0.35,text_opts=list(cex=0.7))