A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Most price indexes are made with a two-step procedure, where
    period-over-period elemental indexes are first calculated for a collection
    of elemental aggregates at each point in time, and then aggregated according
    to a price index aggregation structure. These indexes can then be chained
    together to form a time series that gives the evolution of prices with
    respect to a fixed base period. This package contains a collections of
    functions that revolve around this work flow, making it easy to build
    standard price indexes, and implement the methods described by
    Balk (2008, ISBN:978-1-107-40496-0), von der Lippe (2001,
    ISBN:3-8246-0638-0), and the CPI manual (2020, ISBN:978-1-51354-298-0)
    for bilateral price indexes.

Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.