Tree manipulationFunctions for editing phylogenetic trees. |
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Add a tip to a phylogenetic tree |
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Collapse nodes on a phylogenetic tree |
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Reduced consensus, omitting specified taxa |
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Drop leaves from tree |
Generate a tree with a specified outgroup |
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Force a tree to match a constraint |
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Paths present in reduced tree |
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Identify vertices retained when leaves are dropped |
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Leaf label interchange |
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Generate binary tree by collapsing polytomies |
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Renumber a tree's nodes and tips |
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Renumber a tree's tips |
Root or unroot a phylogenetic tree |
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Sort tree |
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Extract a subtree |
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Generate trivial trees |
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Tree navigationFunctions to navigate phylogenetic trees. |
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Clade sizes |
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Identify descendant edges |
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Ancestors of an edge |
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Distance between edges |
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List ancestors |
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Most recent common ancestor |
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Count descendants for each node in a tree |
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Distance of each node from tree exterior |
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Order of each node in a tree |
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Which node is a tree's root? |
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Tree creationFunctions to generate phylogenetic trees. |
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Constrained neighbour-joining tree |
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Generate pectinate, balanced or random trees |
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Generate a neighbour joining tree |
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Unique integer indices for bifurcating tree topologies |
Generate trivial trees |
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Print |
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Tree propertiesFunctions describing properties of trees. |
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Cladistic information content of a tree |
Construct consensus trees |
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"Stemwardness" of a leaf |
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Total Cophenetic Index |
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Reduced consensus, omitting specified taxa |
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Number of distinct splits |
Number of leaves in a phylogenetic tree |
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Calculate length of paths between each pair of vertices within tree |
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Maximum splits in an n-leaf tree |
Extract tip labels |
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Is tree rooted? |
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Visualize position of rogue taxa |
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Distances between each pair of trees |
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Phylogenetic dataFunctions for modifying and evaluating datasets. |
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Convert between matrices and |
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Convert between strings and |
Artificial Extinction |
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ParsersFunctions to parse or write files. |
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Write a phylogenetic tree in Newick format |
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Read modification time from "ape" Nexus file |
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Extract taxa from a matrix block |
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Write Newick Tree |
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Read phylogenetic characters from file |
Parse TNT Tree |
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Convert between strings and |
Write morphological character matrix to TNT file |
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Add full stop to end of a sentence |
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Decode MorphoBank text |
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Rightmost character of string |
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Remove quotation marks from a string |
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Split manipulationFunctions that manipulate bipartition splits. |
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Drop leaves from tree |
Subset of a split on fewer leaves |
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Identify and remove trivial splits |
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Label splits |
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Number of distinct splits |
Number of leaves in a phylogenetic tree |
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Polarize splits on a single taxon |
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Frequency of splits |
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Convert object to |
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Maximum splits in an n-leaf tree |
Extract tip labels |
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Tips contained within splits |
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Split matching |
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Exclusive OR operation |
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Information and combinatoricsFunctions to calculate factorial quantities. |
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Number of trees one SPR step away |
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Double factorial |
Distributions of tips consistent with a partition pair |
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Cladistic information content of a tree |
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Number of trees |
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Number of trees containing a tree |
Character information content |
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Phylogenetic information content of splitting leaves into two partitions |
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Probability of matching this well |
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Number of trees matching a bipartition split |
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Number of trees consistent with split |
Split supportCalculate and depict support for splits (‘edges’ / ‘nodes’) in trees. |
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Label splits |
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Frequency of splits |
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Colour for node support value |
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DatasetsData that accompanies the package. |
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Brewer palettes |
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Double factorials |
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Data from Zhang et al. 2016 |
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Natural logarithms of double factorials |
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Number of rooted / unrooted tree shapes |
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Utility functionsMiscellaneous functions to simplify or expedite basic functionality. |
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Convert object to |
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Convert phylogenetic tree to |
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S3 methods for |
Hamming distance between taxa in a phylogenetic dataset |
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Minimum spanning tree |
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Rightmost character of string |
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Quickly sample |
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Apply a function that returns 64-bit integers over a list or vector |
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Produce a legend for continuous gradient scales |
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Sort a list of phylogenetic trees |
Add tree to start of list |
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Developer functionsEfficient functions without input checks, for developers |
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Efficiently convert edge matrix to splits |