ape, deSolve, GenSA, subplex, data.table

c(person("Jeremy", "Beaulieu", role=c("aut", "cre"),
email = "jbeaulieu@nimbios.org"),
person("Brian", "O'Meara", role=c("aut")))
Jeremy Beaulieu [aut, cre],
Brian O'Meara [aut]

Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.

c(person("Jeremy", "Beaulieu", role=c("aut", "cre"),
email = "jbeaulieu@nimbios.org"),
person("Brian", "O'Meara", role=c("aut")),
person("Daniel", "Caetano", role=c("aut")))
parallel, phytools, data.table, methods, diversitree
Jeremy Beaulieu [aut, cre],
Brian O'Meara [aut],
Daniel Caetano [aut]

parallel, phytools, data.table, methods, diversitree, plotrix

c(person("Jeremy", "Beaulieu", role=c("aut", "cre"),
email = "jmbeauli@uark.edu"),
person("Brian", "O'Meara", role=c("aut")),
person("Daniel", "Caetano", role=c("aut")),
person("James", "Boyko", role=c("aut")))
Jeremy Beaulieu [aut, cre],
Brian O'Meara [aut],
Daniel Caetano [aut],
James Boyko [aut]

c(person("Jeremy", "Beaulieu", role=c("aut", "cre"),
email = "jbeaulieu@nimbios.org"),
person("Brian", "O'Meara", role=c("aut")),
person("Daniel", "Caetano", role=c("aut")),
person("James", "Boyko", role=c("aut")))

c(person("Jeremy", "Beaulieu", role=c("aut", "cre"),
email = "jmbeauli@uark.edu"),
person("Brian", "O'Meara", role=c("aut")),
person("Daniel", "Caetano", role=c("aut")),
person("James", "Boyko", role=c("aut")),
person("Thais", "Vasconcelos", role=c("aut")))
parallel, phytools, data.table, igraph, methods, diversitree,
paleotree, plotrix, geiger, phangorn, TreeSim, corHMM
Jeremy Beaulieu [aut, cre],
Brian O'Meara [aut],
Daniel Caetano [aut],
James Boyko [aut],
Thais Vasconcelos [aut]

Using the MDL principle, it is possible to estimate
parameters for a histogram-like model. The package contains
the implementation of such an estimation method.

Construction of regular and irregular histograms with different
options for automatic choice of bins
Thoralf Mildenberger, Yves Rozenholc, David Zasada.
Automatic construction of regular and irregular histograms
as described in Rozenholc/Mildenberger/Gather (2009).