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. For more details see Volz and Frost (2017) <doi:10.1093/ve/vex025>.

The model estimates air pollution removal by dry deposition on trees. It also estimates or uses hourly values for aerodynamic resistance, boundary layer resistance, canopy resistance, stomatal resistance, cuticular resistance, mesophyll resistance, soil resistance, friction velocity and deposition velocity. It also allows plotting graphical results for a specific time period. The pollutants are nitrogen dioxide, ozone, sulphur dioxide, carbon monoxide and particulate matter. Baldocchi D (1994) <doi:10.1093/treephys/14.7-8-9.1069>. Farquhar GD, von Caemmerer S, Berry JA (1980) Planta 149: 78-90. Hirabayashi S, Kroll CN, Nowak DJ (2015) i-Tree Eco Dry Deposition Model. Nowak DJ, Crane DE, Stevens JC (2006) <doi:10.1016/j.ufug.2006.01.007>. US EPA (1999) PCRAMMET User's Guide. EPA-454/B-96-001. Weiss A, Norman JM (1985) Agricultural and Forest Meteorology 34: 205—213.

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

Perform test to detect differences in structure between families of
             trees. The method is based on cophenetic distances and aggregated
             Student's tests.

Testing for trajectory presence and heterogeneity on
 multivariate data. Two statistical methods (Tenha & Song 2022) 
 <doi:10.1371/journal.pcbi.1009829> are implemented. The tree dimension
 test quantifies the statistical evidence for trajectory presence. The
 subset specificity measure summarizes pattern heterogeneity using the
 minimum subtree cover. There is no user tunable parameters for either
 method. Examples are included to illustrate how to use the methods on 
 single-cell data for studying gene and pathway expression dynamics and
 pathway expression specificity.