Implementation of unconditional Bernoulli Scan Statistic developed by Kulldorff et al. (2003) <doi:10.1111/1541-0420.00039> for hierarchical tree structures. Tree-based Scan Statistics are an exploratory method to identify event clusters across the space of a hierarchical tree.

This package provides tools for the exploration of distributions of phylogenetic trees. This package includes a shiny interface which can be started from R using treespaceServer(). For further details see Jombart et al. (2017) <DOI:10.1111/1755-0998.12676>.

Create tree structures from hierarchical data, and traverse the tree in various orders. Aggregate, cumulate, print, plot, convert to and from data.frame and more. This is useful for decision trees, machine learning, finance, conversion from and to JSON, and many other applications.

This package provides functions for estimating times of common ancestry and molecular clock rates of evolution using a variety of evolutionary models, parametric and nonparametric bootstrap confidence intervals, methods for detecting outlier lineages, root-to-tip regression, and a statistical test for selecting molecular clock models. The methods are described in Volz, E.M. and S.D.W. Frost (2017) <doi:10.1093/ve/vex025>.

Collection of phylogenetic tree statistics, collected throughout the literature. All functions have been written to maximize computation speed. The package includes umbrella functions to calculate all statistics, all balance associated statistics, or all branching time related statistics. Furthermore, the treestats package supports summary statistic calculations on Ltables, provides speed-improved coding of branching times, Ltable conversion and includes algorithms to create intermediately balanced trees. Full description can be found in Janzen (2024) <doi:10.1016/j.ympev.2024.108168>.

Tree-sitter is a parser generator tool and an incremental parsing library. It can build a concrete syntax tree for a source file and efficiently update the syntax tree as the source file is edited.

Tree-sitter aims to be:

• General enough to parse any programming language

• Fast enough to parse on every keystroke in a text editor

• Robust enough to provide useful results even in the presence of syntax errors

• Dependency-free so that the runtime library (which is written in pure C) can be embedded in any application

This package includes the libtree-sitter runtime library.

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of stemwardness (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.

This package provides a flexible simulation tool for phylogenetic trees under a general model for speciation and extinction. Trees with a user-specified number of extant tips, or a user-specified stem age are simulated. It is possible to assume any probability distribution for the waiting time until speciation and extinction. Furthermore, the waiting times to speciation / extinction may be scaled in different parts of the tree, meaning we can simulate trees with clade-dependent diversification processes. At a speciation event, one species splits into two. We allow for two different modes at these splits: (i) symmetric, where for every speciation event new waiting times until speciation and extinction are drawn for both daughter lineages; and (ii) asymmetric, where a speciation event results in one species with new waiting times, and another that carries the extinction time and age of its ancestor. The symmetric mode can be seen as an vicariant or allopatric process where divided populations suffer equal evolutionary forces while the asymmetric mode could be seen as a peripatric speciation where a mother lineage continues to exist. Reference: O. Hagen and T. Stadler (2017). TreeSimGM: Simulating phylogenetic trees under general Bellman Harris models with lineage-specific shifts of speciation and extinction in R. Methods in Ecology and Evolution. <doi:10.1111/2041-210X.12917>.

This package provides ggplot2 geoms for drawing treemaps.

Generic tools for recursive and iterative tree traversal based on clojure.walk and clojure.zip respectively.

This package provides a Ruby-based Parsing Expression Grammar (PEG) parser generator Domain Specific Language (DSL).

Combine a list of taxa with a phylogeny to generate a starting tree for use in total evidence dating analyses.

This package provides bindings to Tree-sitter', an incremental parsing system for programming tools. Tree-sitter builds concrete syntax trees for source files of any language, and can efficiently update those syntax trees as the source file is edited. It also includes a robust error recovery system that provides useful parse results even in the presence of syntax errors.

Provide a range of functions with multiple criteria for cutting phylogenetic trees at any evolutionary depth. It enables users to cut trees in any orientation, such as rootwardly (from root to tips) and tipwardly (from tips to its root), or allows users to define a specific time interval of interest. It can also be used to create multiple tree pieces of equal temporal width. Moreover, it allows the assessment of novel temporal rates for various phylogenetic indexes, which can be quickly displayed graphically.

The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one.

Reconstruct phylogenetic trees from discrete data. Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy" library, under equal or implied step weights. Contains a "shiny" user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection, tree space mapping, and cluster consensus trees (Smith 2022a, b) <doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>. Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, Successive Approximations (Farris, 1969) <doi:10.2307/2412182> and custom optimality criteria are implemented.

This package provides functionality for creation and comparison of polynomials that uniquely describe trees as introduced in Liu (2019, <arXiv:1904.03332>). The core method converts rooted unlabeled phylo objects from ape to the tree defining polynomials described with coefficient matrices. Additionally, a conversion for rooted binary trees with binary trait labels is also provided. Once the polynomials of trees are calculated there are functions to calculate distances, distance matrices and plot different distance trees from a target tree. Manipulation and conversion to the tree defining polynomials is implemented in C++ with Rcpp and RcppArmadillo'. Furthermore, parallel programming with RcppThread is used to improve performance converting to polynomials and calculating distances.

A tree utility library

Ego Tree provides a vec-backed ID-tree.

This package provides a library for visualizing tree structured data.

This package provides a R grammar for the Tree-sitter library.

This package provides a C grammar for the Tree-sitter library.

Visualizing cuts for either axis-align or non axis-align tree methods (e.g. decision tree, random tessellation process).

The TreeAndLeaf package combines unrooted and force-directed graph algorithms in order to layout binary trees, aiming to represent multiple layers of information onto dendrogram leaves.