[Phylobase-commits] r319 - pkg/man

[noreply at r-forge.r-project.org]

Author: bbolker
Date: 2008-12-19 06:08:22 +0100 (Fri, 19 Dec 2008)
New Revision: 319

Modified:
   pkg/man/as-methods.Rd
   pkg/man/extract.tree.Rd
   pkg/man/phylo4d.Rd
Log:

 various fixes to cope with current plot breakage, labeling changes



Modified: pkg/man/as-methods.Rd
===================================================================
--- pkg/man/as-methods.Rd	2008-12-19 05:07:44 UTC (rev 318)
+++ pkg/man/as-methods.Rd	2008-12-19 05:08:22 UTC (rev 319)
@@ -90,7 +90,7 @@
 as(tree_in_phylo4, "phylog")      # conversion to phylog (ade4)
 as(tree_in_phylo4, "data.frame")  # conversion to data.frame
 as(tree_in_phylo4, "phylo")       # conversion to phylo (ape)
-as(tree_in_phylo4, "phylo4d")     # conversion to phylo4d, but without data so data slots empty.
+as(tree_in_phylo4, "phylo4d")     # conversion to phylo4d, but with data slots empty
 }
 \keyword{methods}
 \concept{phylo4 tree formats}

Modified: pkg/man/extract.tree.Rd
===================================================================
--- pkg/man/extract.tree.Rd	2008-12-19 05:07:44 UTC (rev 318)
+++ pkg/man/extract.tree.Rd	2008-12-19 05:08:22 UTC (rev 319)
@@ -20,10 +20,9 @@
 tree <- as(tree.phylo, "phylo4")
 plot(tree)
 tip.data <- data.frame(size = c(1, 2, 3), row.names = c("a", "b", "c"))
-treedata <- phylo4d(tree, tip.data)
-plot(treedata)
-print(treedata)
-tree1 <- extract.tree(treedata)
-print(tree1)
+(treedata <- phylo4d(tree, tip.data))
+## treePlot(treedata)  ## not yet -- wait for debugging
+(tree1 <- extract.tree(treedata))
+## treePlot(tree1)   ## not yet -- wait for debugging
 }
 \keyword{methods}

Modified: pkg/man/phylo4d.Rd
===================================================================
--- pkg/man/phylo4d.Rd	2008-12-19 05:07:44 UTC (rev 318)
+++ pkg/man/phylo4d.Rd	2008-12-19 05:08:22 UTC (rev 319)
@@ -105,8 +105,9 @@
 geoTree <- as(geoTree, "phylo4")
 
 ## some random node data
-rNodeData <- data.frame(randomTrait = rnorm(nNodes(geoTree)),
-                        row.names = nodeLabels(geoTree))
+rNodeData <- data.frame(randomTrait = rnorm(nNodes(geoTree)))
+## comment out node labels for now (empty)
+##                        row.names = nodeLabels(geoTree))
 
 exGeo2 <- phylo4d(geoTree, tip.data = geoData, node.data = rNodeData)
 
@@ -121,7 +122,9 @@
 
 ### Example with 'all.data'
 rAllData <- data.frame(randomTrait = rnorm(nTips(geoTree) + nNodes(geoTree)),
-                       row.names = c(labels(geoTree), nodeLabels(geoTree)))
+row.names = c(labels(geoTree),nodeNumbers(geoTree)))
+
+
 exGeo5 <- phylo4d(geoTree, all.data = rAllData)