Our method introduces mathematically well-defined measures for tightness of branches in a hierarchical tree. Statistical significance of the findings is determined, for all branches of the tree, by performing permutation tests, optionally with generalized Pareto p-value estimation.

parallel, signal, fdrtool, graphics, stats, utils

TBF Methodology Extension for Multinomial Outcomes
Extends the test-based Bayes factor (TBF) methodology to multinomial regression models and discrete time-to-event models with competing risks. The TBF methodology has been well developed and implemented for the generalised linear model [Held et al. (2015) <doi:10.1214/14-STS510>] and for the Cox model [Held et al. (2016) <doi:10.1002/sim.7089>].
VGAM, nnet, parallel, stats, stringr, plotrix, methods

Rearrangement Distances Between Unrooted Phylogenetic Trees
c(person("Martin R.", 'Smith',
email = "martin.smith@durham.ac.uk",
role = c("aut", "cre", "cph"),
comment = c(ORCID = "0000-0001-5660-1727")),
person(given = "Chris", family = "Whidden",
email = "cwhidden@fredhutch.org", role = c("cph"))
)
Underlying C++ code copyright 2018 Chris Whidden.
Fast calculation of the Subtree Prune and Regraft (SPR),
Tree Bisection and Reconnection (TBR) and Replug distances between
unrooted trees, using the algorithms of Whidden and
Matsen (2017) <arxiv:1511.07529>.
Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Chris Whidden [cph]

ape, Rdpack, TreeDist, TreeTools (>= 1.1.0)

Adriano Polpo <polpo@ufscar.br>, Cassio de Campos
<cassio@idsia.ch>, D. Sinha <sinhad@stat.fsu.edu>, Stuart
Lipsitz <slipsitz@partners.org>, Jianchang Lin
<jlin@stat.fsu.edu>
R (>= 2.14.0), stats, mcmc, coda, survival, normalp, R.utils
This package contais the functions used to perform the
reliability analysis using a parametric Transform-both-sides
(TBS) model.

R (>= 2.15.3), mcmc, coda, survival, normalp, R.utils, BMS
This package contains functions used to perform the
reliability/survival analysis using a parametric
Transform-both-sides (TBS) model.