Companion Package for the Book "Data Integration, Manipulation
and Visualization of Phylogenetic Trees" by Guangchuang Yu
(2022, ISBN:9781032233574)
c(
person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
person("Shuangbin", "Xu",       email = "xshuangbin@163.com",      role = "aut", comment = c(ORCID="0000-0003-3513-5362")),
person("Lin", "Li",             email = "williamlee2220@qq.com",   role = "aut", comment = c(ORCID="0000-0002-6522-1889"))
)
The companion package that provides all the datasets used in the book
"Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574).

A Boosted Tweedie Compound Poisson Model
c(
person("Yi", "Yang", email = "yi.yang6@mcgill.ca",
role = c("aut", "cre"), comment = "http://www.math.mcgill.ca/yyang/"),
person("Hui", "Zou", email = "hzou@stat.umn.edu",
role = c("aut"), comment = "http://users.stat.umn.edu/~zouxx019/"),
person("Wei", "Qian", email = "weiqian@udel.edu",
role = c("aut"), comment = "https://sites.google.com/a/udel.edu/weiqian/"),
person("Greg", "Ridgeway", email = "gregridgeway@gmail.com",
role = c("ctb","cph"))
)
An implementation of a boosted Tweedie compound Poisson model proposed by Yang, Y., Qian, W. and Zou, H. (2018) <doi:10.1080/07350015.2016.1200981>. It is capable of fitting a flexible nonlinear Tweedie compound Poisson model (or a gamma model) and capturing high-order interactions among predictors. This package is based on the 'gbm' package originally developed by Greg Ridgeway.
Yi Yang [aut, cre] (http://www.math.mcgill.ca/yyang/),
Hui Zou [aut] (http://users.stat.umn.edu/~zouxx019/),
Wei Qian [aut] (https://sites.google.com/a/udel.edu/weiqian/),
Greg Ridgeway [ctb, cph]

Insertion/Deletion Dynamics for Transposable Elements
Provides functions to estimate the insertion and deletion rates of transposable element (TE) families. The estimation of insertion rate consists of an improved estimate of the age distribution that takes into account random mutations, and an adjustment by the deletion rate. A hypothesis test for a uniform insertion rate is also implemented. This package implements the methods proposed in Dai et al (2018).
c(person("Xiongtao", "Dai", email="dai@ucdavis.edu",
role=c("aut", "cre", "cph")),
person("Hao", "Wang", role="aut"),
person("Jan", "Dvorak", role="ctb"),
person("Jeffrey", "Bennetzen", role="ctb"),
person("Hans-Georg", "Mueller", role="ctb"))
Xiongtao Dai [aut, cre, cph],
Hao Wang [aut],
Jan Dvorak [ctb],
Jeffrey Bennetzen [ctb],
Hans-Georg Mueller [ctb]