Packaged: 2018-12-02 17:21:30 UTC; silvestre.garcia

Author: Wen Tian (Wendy) Wang,Lloyd Elliott
Maintainer: Wen Tian (Wendy) Wang <wtwang@sfu.ca>
Description: Visualizing cuts for either axis-align or non axis-align tree methods (e.g. decision tree, random tessellation process).
Packaged: 2020-11-10 01:57:21 UTC; wendywang

Packaged: 2021-03-25 10:49:49 UTC; wendywang

Title: Trajectory Presence and Heterogeneity in Multivariate Data
Authors@R: c(person("Lovemore", "Tenha", role = "aut",
Author: Lovemore Tenha [aut] (<https://orcid.org/0000-0001-9705-2023>),
Description: Testing on multivariate data for trajectory presence
and heterogeneity. Two statistical methods (Tenha & Song,
provisionally accepted) are implemented. The tree dimension test
quantifies the statistical evidence for trajectory presence. The
subset specificity measure summarizes pattern heterogeneity using the
minimum subtree cover. There is no user tunable parameters for either
method. Examples are included to illustrate how to use the methods on
single-cell data for studying gene and pathway expression dynamics and
Imports: fitdistrplus, igraph, nFactors, Rcpp (>= 1.0.2), RColorBrewer,

person("Lovemore", "Tenha", , "ltenha@nmsu.edu", role = "aut",
person("Joe", "Song", , "joemsong@cs.nmsu.edu", role = c("aut", "cre"),
Description: Testing for trajectory presence and heterogeneity on
multivariate data. Two statistical methods (Tenha & Song 2022)
<doi:10.1371/journal.pcbi.1009829> are implemented. The tree dimension
test quantifies the statistical evidence for trajectory presence. The

Title: Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith, 2020)
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
Calculates the median of a set of trees under any distance metric.
Copyright: Incorporates Jonker-Volgenant Linear Assignment Problem
implementation by Roy Jonker, modified by Yong Yang after Yi
Imports: ape (>= 5.0), colorspace, memoise, phangorn (>= 2.2.1),
Suggests: bookdown, cluster, kdensity, knitr, MASS, Quartet, rmarkdown,
Rcpp, Rdpack, testthat, Ternary (>= 1.1.2), TreeDistData (>
Author: Martin R. Smith [aut, cre, cph, prg]