Melyssa Minto, Michele Josey, and ClarLynda Williams-DeVane
Various imputation methods are utilized in this package, where one can flag and impute non-monotonic data that is outside of a prespecified range.
compare, doParallel, foreach, iterators, parallel

Allows to Explore Monophyly (or Lack of it) of Taxonomic Groups
in a Phylogeny
ape, phytools, phangorn, RColorBrewer, taxize
Requires rooted resolved 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.

Explore Monophyly of Taxonomic Groups in a Phylogeny
c(person("Orlando", "Schwery", role=c("aut", "cre"), email="oschwery@vols.utk.edu"),
person("Brian C.", "O'Meara", role=c("aut", "ctb")),
person("Peter", "Cowman", role=c("ctb")))
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>.
Orlando Schwery [aut, cre],
Brian C. O'Meara [aut, ctb],
Peter Cowman [ctb]

c(person(c("Berwin", "A."), "Turlach",
role=c("aut", "cre"),
email = "Berwin.Turlach@gmail.com"),
person("Kevin", "Murray",
role="ctb",
email = "Kevin.Murray@uwa.edu.au")
)
Functions for fitting monotone polynomials to data.
Berwin A. Turlach [aut, cre],
Kevin Murray [ctb]

c(person(c("Berwin", "A."), "Turlach", role=c("aut", "cre"),
email = "Berwin.Turlach@gmail.com"), person("Kevin", "Murray",
role="ctb", email = "Kevin.Murray@uwa.edu.au") )
Package contains functions to fit monotone polynomials to
data
Berwin A. Turlach [aut, cre], Kevin Murray [ctb]

c(person(c("Berwin", "A."), "Turlach",
role=c("aut", "cre"),
email = "Berwin.Turlach@gmail.com",
comment=c(ORCID = "0000-0001-8795-471X")),
person("Kevin", "Murray",
role="ctb",
email = "Kevin.Murray@uwa.edu.au",
comment=c(ORCID = "0000-0002-8856-6046"))
)
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>.