Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DNAbin2index.Rd: DNAbin
  EmptyCells.Rd: DNAbin
  code.simple.gaps.Rd: DNAbin
  collapseUnsupportedEdges.Rd: phylo
  combMyTree.Rd: phylo
  del.miss.Rd: DNAbin
  deleteGaps.Rd: DNAbin
  fixNodes.Rd: phylo, read.nexus
  forceEqualTipHeights.Rd: is.ultrametric, chronos
  index2DNAbin.Rd: DNAbin
  ips-package.Rd: ladderize, rotate
  ips.16S.Rd: DNAbin
  ips.28S.Rd: DNAbin
  ips.cox1.Rd: DNAbin
  mafft.Rd: phylo
  mafft.merge.Rd: DNAbin, AAbin, phylo
  mrbayes.Rd: DNAbin
  multistate.Rd: ace
  neighboringPairs.Rd: mst
  ntip.Rd: phylo
  pathd8.Rd: phylo
  phylo2mafft.Rd: phylo
  phylo2mst.Rd: phylo
  pis.Rd: DNAbin
  raxml.Rd: DNAbin, phylo
  raxml.partitions.Rd: DNAbin, cbind.DNAbin
  rbeauti.Rd: DNAbin
  read.Rd: cbind.DNAbin
  sister.Rd: phylo
  splitIntoClades.Rd: phylo
  terminalSisters.Rd: phylo
  tipHeights.Rd: phylo, branching.times
  traitRate.Rd: phylo, DNAbin, read.tree
  write.fas.Rd: DNAbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DNAbin2index.Rd: DNAbin
  EmptyCells.Rd: DNAbin
  code.simple.gaps.Rd: DNAbin
  collapseUnsupportedEdges.Rd: phylo
  combMyTree.Rd: phylo
  del.miss.Rd: DNAbin
  deleteGaps.Rd: DNAbin
  fixNodes.Rd: phylo, read.nexus
  forceEqualTipHeights.Rd: is.ultrametric, chronos
  index2DNAbin.Rd: DNAbin
  ips-package.Rd: ladderize, rotate
  ips.16S.Rd: DNAbin
  ips.28S.Rd: DNAbin
  ips.cox1.Rd: DNAbin
  mafft.Rd: phylo
  mafft.merge.Rd: DNAbin, AAbin, phylo
  mrbayes.Rd: DNAbin
  multistate.Rd: ace
  neighboringPairs.Rd: mst
  ntip.Rd: phylo
  pathd8.Rd: phylo
  phylo2mafft.Rd: phylo
  phylo2mst.Rd: phylo
  pis.Rd: DNAbin
  raxml.Rd: DNAbin, phylo
  raxml.partitions.Rd: DNAbin, cbind.DNAbin
  rbeauti.Rd: DNAbin
  read.Rd: cbind.DNAbin
  sister.Rd: phylo
  splitIntoClades.Rd: phylo
  terminalSisters.Rd: phylo
  tipHeights.Rd: phylo, branching.times
  traitRate.Rd: phylo, DNAbin, read.tree
  write.fas.Rd: DNAbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DNAbin2index.Rd: DNAbin
  EmptyCells.Rd: DNAbin
  code.simple.gaps.Rd: DNAbin
  collapseUnsupportedEdges.Rd: phylo
  combMyTree.Rd: phylo
  del.miss.Rd: DNAbin
  deleteGaps.Rd: DNAbin
  fixNodes.Rd: phylo, read.nexus
  forceEqualTipHeights.Rd: is.ultrametric, chronos
  index2DNAbin.Rd: DNAbin
  ips-package.Rd: ladderize, rotate
  ips.16S.Rd: DNAbin
  ips.28S.Rd: DNAbin
  ips.cox1.Rd: DNAbin
  mafft.Rd: phylo
  mafft.merge.Rd: DNAbin, AAbin, phylo
  mrbayes.Rd: DNAbin
  multistate.Rd: ace
  neighboringPairs.Rd: mst
  ntip.Rd: phylo
  pathd8.Rd: phylo
  phylo2mafft.Rd: phylo
  phylo2mst.Rd: phylo
  pis.Rd: DNAbin
  raxml.Rd: DNAbin, phylo
  raxml.partitions.Rd: DNAbin, cbind.DNAbin
  rbeauti.Rd: DNAbin
  read.Rd: cbind.DNAbin
  sister.Rd: phylo
  splitIntoClades.Rd: phylo
  terminalSisters.Rd: phylo
  tipHeights.Rd: phylo, branching.times
  traitRate.Rd: phylo, DNAbin, read.tree
  write.fas.Rd: DNAbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DNAbin2index.Rd: DNAbin
  EmptyCells.Rd: DNAbin
  code.simple.gaps.Rd: DNAbin
  collapseUnsupportedEdges.Rd: phylo
  combMyTree.Rd: phylo
  del.miss.Rd: DNAbin
  deleteGaps.Rd: DNAbin
  fixNodes.Rd: phylo, read.nexus
  forceEqualTipHeights.Rd: is.ultrametric, chronos
  index2DNAbin.Rd: DNAbin
  ips-package.Rd: ladderize, rotate
  ips.16S.Rd: DNAbin
  ips.28S.Rd: DNAbin
  ips.cox1.Rd: DNAbin
  mafft.Rd: phylo
  mafft.merge.Rd: DNAbin, AAbin, phylo
  mrbayes.Rd: DNAbin
  multistate.Rd: ace
  neighboringPairs.Rd: mst
  ntip.Rd: phylo
  pathd8.Rd: phylo
  phylo2mafft.Rd: phylo
  phylo2mst.Rd: phylo
  pis.Rd: DNAbin
  raxml.Rd: DNAbin, phylo
  raxml.partitions.Rd: DNAbin, cbind.DNAbin
  rbeauti.Rd: DNAbin
  read.Rd: cbind.DNAbin
  sister.Rd: phylo
  splitIntoClades.Rd: phylo
  terminalSisters.Rd: phylo
  tipHeights.Rd: phylo, branching.times
  traitRate.Rd: phylo, DNAbin, read.tree
  write.fas.Rd: DNAbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DNAbin2index.Rd: DNAbin
  EmptyCells.Rd: DNAbin
  code.simple.gaps.Rd: DNAbin
  collapseUnsupportedEdges.Rd: phylo
  combMyTree.Rd: phylo
  del.miss.Rd: DNAbin
  deleteGaps.Rd: DNAbin
  fixNodes.Rd: phylo, read.nexus
  forceEqualTipHeights.Rd: is.ultrametric, chronos
  index2DNAbin.Rd: DNAbin
  ips-package.Rd: ladderize, rotate
  ips.16S.Rd: DNAbin
  ips.28S.Rd: DNAbin
  ips.cox1.Rd: DNAbin
  mafft.Rd: phylo
  mafft.merge.Rd: DNAbin, AAbin, phylo
  mrbayes.Rd: DNAbin
  multistate.Rd: ace
  neighboringPairs.Rd: mst
  ntip.Rd: phylo
  pathd8.Rd: phylo
  phylo2mafft.Rd: phylo
  phylo2mst.Rd: phylo
  pis.Rd: DNAbin
  raxml.Rd: DNAbin, phylo
  raxml.partitions.Rd: DNAbin, cbind.DNAbin
  rbeauti.Rd: DNAbin
  read.Rd: cbind.DNAbin
  sister.Rd: phylo
  splitIntoClades.Rd: phylo
  terminalSisters.Rd: phylo
  tipHeights.Rd: phylo, branching.times
  traitRate.Rd: phylo, DNAbin, read.tree
  write.fas.Rd: DNAbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DNAbin2index.Rd: DNAbin
  EmptyCells.Rd: DNAbin
  code.simple.gaps.Rd: DNAbin
  collapseUnsupportedEdges.Rd: phylo
  combMyTree.Rd: phylo
  del.miss.Rd: DNAbin
  deleteGaps.Rd: DNAbin
  fixNodes.Rd: phylo, read.nexus
  forceEqualTipHeights.Rd: is.ultrametric, chronos
  index2DNAbin.Rd: DNAbin
  ips-package.Rd: ladderize, rotate
  ips.16S.Rd: DNAbin
  ips.28S.Rd: DNAbin
  ips.cox1.Rd: DNAbin
  mafft.Rd: phylo
  mafft.merge.Rd: DNAbin, AAbin, phylo
  mrbayes.Rd: DNAbin
  multistate.Rd: ace
  neighboringPairs.Rd: mst
  ntip.Rd: phylo
  pathd8.Rd: phylo
  phylo2mafft.Rd: phylo
  phylo2mst.Rd: phylo
  pis.Rd: DNAbin
  raxml.Rd: DNAbin, phylo
  raxml.partitions.Rd: DNAbin, cbind.DNAbin
  rbeauti.Rd: DNAbin
  read.Rd: cbind.DNAbin
  sister.Rd: phylo
  splitIntoClades.Rd: phylo
  terminalSisters.Rd: phylo
  tipHeights.Rd: phylo, branching.times
  traitRate.Rd: phylo, DNAbin, read.tree
  write.fas.Rd: DNAbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.