ape, seqinr, stringr, kmer, DECIPHER, beepr, Biostrings,
grDevices, doParallel, foreach, parallel

Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver
<jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
ape, nloptr, numDeriv, expm, corpcor, phangorn, parallel,
rgenoud
Fits a hidden rates model that allows different transition
rate classes on different portions of a phylogeny by treating
rate classes as hidden states in a Markov process and various
other functions for evaluating models of binary character
evolution.

Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
expm, numDeriv, corpcor, phangorn, rgenoud
Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.

expm, numDeriv, corpcor, phangorn, rgenoud, parallel

expm, numDeriv, corpcor, phangorn, parallel

expm, numDeriv, corpcor, nnet, phangorn, parallel, Rmpfr
Fits a hidden rates model that allows different transition rate
classes on different portions of a phylogeny by treating rate classes as hidden
states in a Markov process and various other functions for evaluating models of
binary character evolution.

Hidden Markov Models of Character Evolution
c(person("Jeremy", "Beaulieu", role=c("aut", "cre"),
email = "jmbeauli@uark.edu"),
person("Brian", "O'Meara", role=c("aut")),
person("Jeffrey", "Oliver", role=c("aut")),
person("James", "Boyko", role=c("aut")))
expm, numDeriv, corpcor, MASS, nnet, phangorn, parallel,
viridis, Rmpfr, igraph, phytools
Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.
Jeremy Beaulieu [aut, cre],
Brian O'Meara [aut],
Jeffrey Oliver [aut],
James Boyko [aut]

Significance Testing of Rank Cross-Correlations under SRD
c(person("David", "Lun", role=c("aut", "cre"), email="lun@hydro.tuwien.ac.at"),
person("Svenja", "Fischer", role=c("aut"), email="Svenja.Fischer@hydrology.ruhr-uni-bochum.de"),
person("Alberto", "Viglione", role=c("aut"), email="alberto.viglione@polito.it"))
Significance test of Spearman's Rho or Kendall's Tau
between short-range dependent random variables.
David Lun [aut, cre],
Svenja Fischer [aut],
Alberto Viglione [aut]