Requires rooted phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc. Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways. 
 "MonoPhy: a simple R package to find and visualize monophyly issues." Schwery, O. & O'Meara, B.C. (2016) <doi:10.7717/peerj-cs.56>.

Functions for fitting monotone polynomials to data.
             Detailed discussion of the methodologies used can be
             found in Murray, Mueller and Turlach (2013)
             <doi:10.1007/s00180-012-0390-5> and Murray, Mueller and
             Turlach (2016) <doi:10.1080/00949655.2016.1139582>.

An extended version of the nonparametric Bayesian monotonic regression procedure described in Saarela & Arjas (2011) <DOI:10.1111/j.1467-9469.2010.00716.x>, allowing for multiple additive monotonic components in the linear predictor, and time-to-event outcomes through case-base sampling. The extension and its applications, including estimation of absolute risks, are described in Saarela & Arjas (2015) <DOI:10.1111/sjos.12125>. The package also implements the nonparametric ordinal regression model described in Saarela, Rohrbeck & Arjas <DOI:10.1214/22-BA1310>.

The monotone package contains a fast up-and-down-blocks implementation for the pool-adjacent-violators algorithm 
  for simple linear ordered monotone regression, including two spin-off functions
  for unimodal and bivariate monotone regression (see <doi:10.18637/jss.v102.c01>).

Nonparametric estimation and inference of a non-decreasing monotone hazard
    ratio from a right censored survival dataset.  The
    estimator is based on a generalized Grenander typed estimator, and the
    inference procedure relies on direct plugin estimation of a first order derivative.  More
    details please refer to the paper "Nonparametric inference under a monotone
    hazard ratio order" by Y. Wu and T. Westling (2023) <doi:10.1214/23-EJS2173>.