[Phylobase-commits] r951 - in pkg: . man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu May 8 16:46:53 CEST 2014 

Author: francois
Date: 2014-05-08 16:46:52 +0200 (Thu, 08 May 2014)
New Revision: 951

Modified:
   pkg/NAMESPACE
   pkg/man/MRCA.Rd
   pkg/man/ancestors.Rd
   pkg/man/checkPhylo4.Rd
   pkg/man/edgeLength-methods.Rd
   pkg/man/edges-accessors.Rd
   pkg/man/extractTree.Rd
   pkg/man/formatData.Rd
   pkg/man/geospiza.Rd
   pkg/man/getNode-methods.Rd
   pkg/man/labels-methods.Rd
   pkg/man/multiPhylo-class.Rd
   pkg/man/nTips-methods.Rd
   pkg/man/nodeId-methods.Rd
   pkg/man/owls4.Rd
   pkg/man/pdata-class.Rd
   pkg/man/pdata.Rd
   pkg/man/phylo4-class.Rd
   pkg/man/phylo4-methods.Rd
   pkg/man/phylo4d-accessors.Rd
   pkg/man/phylo4d-class.Rd
   pkg/man/phylo4d-methods.Rd
   pkg/man/phyloXXYY.Rd
   pkg/man/phylobase-package.Rd
   pkg/man/phylobase.options.Rd
   pkg/man/phylobubbles.Rd
   pkg/man/phylomat-class.Rd
   pkg/man/plotOneTree.Rd
   pkg/man/print-methods.Rd
   pkg/man/readNexus.Rd
   pkg/man/reorder-methods.Rd
   pkg/man/root-methods.Rd
   pkg/man/setAs-methods.Rd
   pkg/man/shortestPath-methods.Rd
   pkg/man/subset-methods.Rd
   pkg/man/summary-methods.Rd
   pkg/man/tdata-methods.Rd
   pkg/man/tip.data.plot.Rd
   pkg/man/treePlot-methods.Rd
   pkg/man/treeStructure-methods.Rd
Log:
update docs, and NAMESPACE after bug fix in roxygen2

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/NAMESPACE	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,3 +1,5 @@
+# Generated by roxygen2 (4.0.0.99): do not edit by hand
+
 export("edgeLabels<-")
 export("edgeLength<-")
 export("labels<-")

Modified: pkg/man/MRCA.Rd
===================================================================
--- pkg/man/MRCA.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/MRCA.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{MRCA}
 \alias{MRCA}

Modified: pkg/man/ancestors.Rd
===================================================================
--- pkg/man/ancestors.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/ancestors.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \name{ancestor}
 \alias{ancestor}
 \alias{ancestors}

Modified: pkg/man/checkPhylo4.Rd
===================================================================
--- pkg/man/checkPhylo4.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/checkPhylo4.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \name{checkPhylo4}
 \alias{checkPhylo4}
 \alias{checkPhylo4Data}

Modified: pkg/man/edgeLength-methods.Rd
===================================================================
--- pkg/man/edgeLength-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/edgeLength-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{hasEdgeLength}
 \alias{depthTips}

Modified: pkg/man/edges-accessors.Rd
===================================================================
--- pkg/man/edges-accessors.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/edges-accessors.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{edges}
 \alias{edgeOrder}

Modified: pkg/man/extractTree.Rd
===================================================================
--- pkg/man/extractTree.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/extractTree.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \name{extractTree}
 \alias{extractTree}
 \title{Get tree from tree+data object}

Modified: pkg/man/formatData.Rd
===================================================================
--- pkg/man/formatData.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/formatData.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \name{formatData}
 \alias{formatData}
 \title{Format data for use in phylo4d objects}

Modified: pkg/man/geospiza.Rd
===================================================================
--- pkg/man/geospiza.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/geospiza.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{data}
 \name{geospiza}
 \alias{geospiza}

Modified: pkg/man/getNode-methods.Rd
===================================================================
--- pkg/man/getNode-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/getNode-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{getNode}
 \alias{getEdge}

Modified: pkg/man/labels-methods.Rd
===================================================================
--- pkg/man/labels-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/labels-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{phylo4-labels}
 \alias{edgeLabels}

Modified: pkg/man/multiPhylo-class.Rd
===================================================================
--- pkg/man/multiPhylo-class.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/multiPhylo-class.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{class}
 \name{multiPhylo-class}
 \alias{multiPhylo-class}

Modified: pkg/man/nTips-methods.Rd
===================================================================
--- pkg/man/nTips-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/nTips-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{nTips}
 \alias{nEdges}

Modified: pkg/man/nodeId-methods.Rd
===================================================================
--- pkg/man/nodeId-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/nodeId-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{nodeId}
 \alias{edgeId}

Modified: pkg/man/owls4.Rd
===================================================================
--- pkg/man/owls4.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/owls4.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{data}
 \name{owls4}
 \alias{owls4}

Modified: pkg/man/pdata-class.Rd
===================================================================
--- pkg/man/pdata-class.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/pdata-class.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{class}
 \name{pdata-class}
 \alias{[,pdata,ANY,ANY,ANY-method}

Modified: pkg/man/pdata.Rd
===================================================================
--- pkg/man/pdata.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/pdata.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \name{pdata}
 \alias{check_pdata}
 \alias{pdata}

Modified: pkg/man/phylo4-class.Rd
===================================================================
--- pkg/man/phylo4-class.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/phylo4-class.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{class}
 \name{phylo4-class}
 \alias{phylo4-class}

Modified: pkg/man/phylo4-methods.Rd
===================================================================
--- pkg/man/phylo4-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/phylo4-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{phylo4-methods}
 \alias{phylo4}

Modified: pkg/man/phylo4d-accessors.Rd
===================================================================
--- pkg/man/phylo4d-accessors.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/phylo4d-accessors.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{hasTipData}
 \alias{hasNodeData}

Modified: pkg/man/phylo4d-class.Rd
===================================================================
--- pkg/man/phylo4d-class.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/phylo4d-class.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{class}
 \name{phylo4d-class}
 \alias{phylo4d-class}

Modified: pkg/man/phylo4d-methods.Rd
===================================================================
--- pkg/man/phylo4d-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/phylo4d-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{phylo4d}
 \alias{phylo4d}

Modified: pkg/man/phyloXXYY.Rd
===================================================================
--- pkg/man/phyloXXYY.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/phyloXXYY.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \name{phyloXXYY}
 \alias{phyloXXYY}
 \title{Calculate node x and y coordinates}

Modified: pkg/man/phylobase-package.Rd
===================================================================
--- pkg/man/phylobase-package.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/phylobase-package.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{package}
 \name{phylobase-package}
 \alias{phylobase}

Modified: pkg/man/phylobase.options.Rd
===================================================================
--- pkg/man/phylobase.options.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/phylobase.options.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \name{phylobase.options}
 \alias{phylobase.options}
 \title{Set or return options of phylobase}

Modified: pkg/man/phylobubbles.Rd
===================================================================
--- pkg/man/phylobubbles.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/phylobubbles.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \name{phylobubbles}
 \alias{phylobubbles}
 \title{Bubble plots for phylo4d objects}

Modified: pkg/man/phylomat-class.Rd
===================================================================
--- pkg/man/phylomat-class.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/phylomat-class.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{class}
 \name{phylomat-class}
 \alias{as_phylo4vcov}

Modified: pkg/man/plotOneTree.Rd
===================================================================
--- pkg/man/plotOneTree.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/plotOneTree.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \name{plotOneTree}
 \alias{plotOneTree}
 \title{Plot a phylo4 object}

Modified: pkg/man/print-methods.Rd
===================================================================
--- pkg/man/print-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/print-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{print}
 \alias{head}

Modified: pkg/man/readNexus.Rd
===================================================================
--- pkg/man/readNexus.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/readNexus.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{Import Nexus and Newick files}
 \alias{Import Nexus and Newick files}

Modified: pkg/man/reorder-methods.Rd
===================================================================
--- pkg/man/reorder-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/reorder-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{reorder-methods}
 \alias{reorder}

Modified: pkg/man/root-methods.Rd
===================================================================
--- pkg/man/root-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/root-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{isRooted}
 \alias{isRooted}

Modified: pkg/man/setAs-methods.Rd
===================================================================
--- pkg/man/setAs-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/setAs-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{setAs}
 \alias{as}

Modified: pkg/man/shortestPath-methods.Rd
===================================================================
--- pkg/man/shortestPath-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/shortestPath-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{shortestPath}
 \alias{shortestPath}

Modified: pkg/man/subset-methods.Rd
===================================================================
--- pkg/man/subset-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/subset-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{subset-methods}
 \alias{[}

Modified: pkg/man/summary-methods.Rd
===================================================================
--- pkg/man/summary-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/summary-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{summary-methods}
 \alias{nodeType}

Modified: pkg/man/tdata-methods.Rd
===================================================================
--- pkg/man/tdata-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/tdata-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{tdata}
 \alias{nodeData}

Modified: pkg/man/tip.data.plot.Rd
===================================================================
--- pkg/man/tip.data.plot.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/tip.data.plot.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \name{tip.data.plot}
 \alias{tip.data.plot}
 \title{Plotting trees and associated data}

Modified: pkg/man/treePlot-methods.Rd
===================================================================
--- pkg/man/treePlot-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/treePlot-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{treePlot-methods}
 \alias{plot}

Modified: pkg/man/treeStructure-methods.Rd
===================================================================
--- pkg/man/treeStructure-methods.Rd	2014-05-08 13:40:05 UTC (rev 950)
+++ pkg/man/treeStructure-methods.Rd	2014-05-08 14:46:52 UTC (rev 951)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
+% Generated by roxygen2 (4.0.0.99): do not edit by hand
 \docType{methods}
 \name{hasSingle}
 \alias{hasPoly}

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