Functions to read and write APE-compatible phylogenetic
trees in NEXUS and Newick formats, while preserving annotations.
'utility.R' 'tokenize.R' 'newick.R' 'nexus.R' 'format.R'

'utility.R' 'tokenize.R' 'newick.R' 'nexus.R' 'format.R'
'mbattrs.R'

Jinlong Zhang, Xiangcheng Mi, Nancai Pei
Tools for phylogenetic analysis espetially for DNA
barcoding and community ecology.

Tools for manupulating DNA sequences for DNA-barcoding,
especially for building supermatrix.

Jinlong Zhang, Nancai Pei, Xiangcheng Mi
Building supermatrix for DNA barcodes using different
genes, calculating the inequality among lineages and
phylogenetic similarity for very large dataset using slicing
methods by invoking Phylocom.

c(person("Jinlong", "Zhang", role = c("aut", "cre"), email = "jinlongzhang01@gmail.com"),
person("Nancai", "Pei", role = c("ctb")),
person("Xiangcheng", "Mi", role = c("ctb")))
Jinlong Zhang [aut, cre],
Nancai Pei [ctb],
Xiangcheng Mi [ctb]
A collection of tools for building RAxML supermatrix using
PHYLIP or aligned FASTA files. These functions will be
useful for building large phylogenies using multiple markers.

Use topological or taxonomic information to maximize the overlap of phylogenetic and comparative data.
Rich FitzJohn, Matt Pennell and Will Cornwell

c(
person("Anthony", "Ives", , "arives@wisc.edu", role = c("aut")),
person("Russell", "Dinnage", , "r.dinnage@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0003-0846-2819")),
person(c("Lucas", "A."), "Nell", , "lucas@lucasnell.com", role = c("aut"), comment = c(ORCID = "0000-0003-3209-0517")),
person("Matthew", "Helmus", , "mrhelmus@temple.edu", role = c("aut")),
person("Daijiang", "Li", , "daijianglee@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0925-3421")))
A collection of functions to do model-based phylogenetic analysis.
It includes functions to calculate community phylogenetic diversity,
to estimate correlations among functional traits while accounting for
phylogenetic relationships, and to fit phylogenetic generalized linear
mixed models. The Bayesian phylogenetic generalized linear mixed models
are fitted with the 'INLA' package (<http://www.r-inla.org>).
stats, ape, Rcpp, Matrix, methods, graphics, dplyr, lme4,
nloptr, gridExtra, mvtnorm, latticeExtra
testthat, pez, tidyr, knitr, rmarkdown, covr, picante,
rbenchmark, INLA, MCMCglmm, logistf, phylolm
Anthony Ives [aut],
Russell Dinnage [aut] (<https://orcid.org/0000-0003-0846-2819>),
Lucas A. Nell [aut] (<https://orcid.org/0000-0003-3209-0517>),
Matthew Helmus [aut],
Daijiang Li [aut, cre] (<https://orcid.org/0000-0002-0925-3421>)