AddTip | Add a tip to a phylogenetic tree |
AncestorEdge | Ancestral edge |
ApeTime | Read modification time from "ape" Nexus file |
ArtificialExtinction | Artificial Extinction |
as.multiPhylo | Convert object to 'multiPhylo' class |
as.Newick | Write a phylogenetic tree in Newick format |
brewer | Brewer palettes |
CharacterInformation | Character information content |
CladeSizes | Clade sizes |
CladisticInfo | Cladistic information content of a tree |
ClusterTable | Convert phylogenetic tree to 'ClusterTable' |
ClusterTable-methods | S3 methods for 'ClusterTable' objects |
CollapseNode | Collapse nodes on a phylogenetic tree |
CompatibleSplits | Which splits are compatible? |
Consensus | Construct consensus trees |
ConsensusWithout | Reduced consensus, omitting specified taxa |
ConstrainedNJ | Constrained neighbour-joining tree |
DescendantEdges | Identify descendant edges |
dot-RandomParent | Random parent vector |
DoubleFactorial | Double factorial |
doubleFactorials | Double factorials |
DropTip | Drop leaves from tree |
EdgeAncestry | Ancestors of an edge |
EdgeDistances | Distance between edges |
edge_to_splits | Efficiently convert edge matrix to splits |
EndSentence | Add full stop to end of a sentence |
EnforceOutgroup | Generate a tree with a specified outgroup |
ExtractTaxa | Extract taxa from a matrix block |
GenerateTree | Generate pectinate, balanced or random trees |
Hamming | Hamming distance between taxa in a phylogenetic dataset |
ImposeConstraint | Force a tree to match a constraint |
is.TreeNumber | Is an object a 'TreeNumber' object? |
J1Index | Robust universal tree balance index |
KeptPaths | Paths present in reduced tree |
KeptVerts | Identify vertices retained when leaves are dropped |
LabelSplits | Label splits |
LeafLabelInterchange | Leaf label interchange |
ListAncestors | List ancestors |
Lobo.data | Data from Zhang et al. 2016 |
logDoubleFactorials | Natural logarithms of double factorials |
MakeTreeBinary | Generate binary tree by collapsing polytomies |
MatchEdges | Match nodes and edges between trees |
match.Splits | Split matching |
MatrixToPhyDat | Convert between matrices and 'phyDat' objects |
MorphoBankDecode | Decode MorphoBank text |
MRCA | Most recent common ancestor |
MSTEdges | Minimum spanning tree |
N1Spr | Number of trees one SPR step away |
NDescendants | Count descendants for each node in a tree |
NewickTree | Write Newick Tree |
Neworder | Reorder edges of a phylogenetic tree |
NJTree | Generate a neighbour joining tree |
NodeDepth | Distance of each node from tree exterior |
NodeNumbers | Numeric index of each node in a tree 'NodeNumbers()' returns... |
NodeOrder | Number of edges incident to each node in a tree |
NPartitionPairs | Distributions of tips consistent with a partition pair |
NRooted | Number of trees |
nRootedShapes | Number of rooted / unrooted tree shapes |
NSplits | Number of distinct splits |
NTip | Number of leaves in a phylogenetic tree |
PairwiseDistances | Distances between each pair of trees |
PathLengths | Calculate length of paths between each pair of vertices... |
PhyToString | Convert between strings and 'phyDat' objects |
PolarizeSplits | Polarize splits on a single taxon |
print.TreeNumber | Print 'TreeNumber' object |
ReadCharacters | Read phylogenetic characters from file |
ReadMrBayesTrees | Read posterior tree sample produced by MrBayes |
ReadTntTree | Parse TNT Tree |
Renumber | Renumber a tree's nodes and tips |
RenumberTips | Renumber a tree's tips |
Reorder | Reorder tree edges and nodes |
RightmostCharacter | Rightmost character of string |
RoguePlot | Visualize position of rogue taxa |
RootNode | Which node is a tree's root? |
root_on_node | Wrapper for internal C function 'root_on_node()' |
RootTree | Root or unroot a phylogenetic tree |
SampleOne | Quickly sample |
sapply64 | Apply a function that returns 64-bit integers over a list or... |
sort.multiPhylo | Sort a list of phylogenetic trees |
SortTree | Sort tree |
SpectrumLegend | Produce a legend for continuous gradient scales |
SplitFrequency | Frequency of splits |
SplitInformation | Phylogenetic information content of splitting leaves into two... |
SplitMatchProbability | Probability of matching this well |
Splits | Convert object to 'Splits' |
SplitsInBinaryTree | Maximum splits in an _n_-leaf tree |
Stemwardness | "Stemwardness" of a leaf |
Subsplit | Subset of a split on fewer leaves |
Subtree | Extract a subtree |
SupportColour | Colour for node support value |
TipLabels | Extract tip labels |
TipsInSplits | Tips contained within splits |
TipTimedTree | Display time-calibrated tree using tip information only |
TopologyOnly | Remove metadata from trees |
TotalCopheneticIndex | Total Cophenetic Index |
TreeIsRooted | Is tree rooted? |
TreeNumber | Unique integer indices for bifurcating tree topologies |
TreeShape | Integer representing shape of a tree |
TreesMatchingSplit | Number of trees matching a bipartition split |
TreesMatchingTree | Number of trees containing a tree |
TreeTools-package | TreeTools |
TrivialSplits | Identify and remove trivial splits |
TrivialTree | Generate trivial trees |
Unquote | Remove quotation marks from a string |
UnrootedTreesMatchingSplit | Number of trees consistent with split |
UnshiftTree | Add tree to start of list |
WriteTntCharacters | Write morphological character matrix to TNT file |
xor | Exclusive OR operation |
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