R: Maximum Likelihood Inference on Multi-State Trees

ML.MSBD-package {ML.MSBD}

R Documentation

Maximum Likelihood Inference on Multi-State Trees

Description

Inference of a multi-states birth-death model from a phylogeny, comprising a number of states N, birth and death rates for each state and on which edges each state appears. Inference is done using a hybrid approach: states are progressively added in a greedy approach. For a fixed number of states N the best model is selected via maximum likelihood. Reference: J. Barido-Sottani, T. G. Vaughan and T. Stadler (2018) <doi:10.1098/rsif.2018.0512>.

Details

Package:	ML.MSBD
Type:	Package
Title:	Maximum Likelihood Inference on Multi-State Trees
Version:	1.2.1
Authors@R:	person("Joelle", "Barido-Sottani", email = "joelle.barido-sottani@m4x.org", role = c("aut", "cre"))
Description:	Inference of a multi-states birth-death model from a phylogeny, comprising a number of states N, birth and death rates for each state and on which edges each state appears. Inference is done using a hybrid approach: states are progressively added in a greedy approach. For a fixed number of states N the best model is selected via maximum likelihood. Reference: J. Barido-Sottani, T. G. Vaughan and T. Stadler (2018) <doi:10.1098/rsif.2018.0512>.
License:	GPL-3
Imports:	ape (>= 5.1), foreach
Suggests:	knitr, rmarkdown, doParallel
RoxygenNote:	6.1.1
VignetteBuilder:	knitr
Author:	Joelle Barido-Sottani [aut, cre]
Maintainer:	Joelle Barido-Sottani <joelle.barido-sottani@m4x.org>

Index of help topics:

ML.MSBD-package         Maximum Likelihood Inference on Multi-State
                        Trees
ML_MSBD                 Full Maximum Likelihood inference of birth and
                        death rates together with their changes along a
                        phylogeny under a multi-type birth-death model.
likelihood_MSBD         Likelihood calculation for randomly sampled
                        trees
likelihood_MSBD_unresolved
                        Likelihood calculation for unresolved trees

Author(s)

Maintainer: NA

References

J. Barido-Sottani and T. Stadler. Accurate detection of HIV transmission clusters from phylogenetic trees using a multi-state birth-death model, BioRXiv 2017. (https://www.biorxiv.org/content/early/2017/11/10/215491)

Examples

# Simulate a random phylogeny
set.seed(25)
tree <- ape::rtree(10)

# Calculate the log likelihood under a multi-states model with 2 states 
# and full extant & extinct sampling
likelihood_MSBD(tree, shifts = matrix(c(2,1.8,2), nrow = 1), 
  gamma = 0.05, lambdas = c(10, 6), mus = c(1, 0.5), sigma = 1)

# Infer the most likely multi-states birth-death model with full extant & extinct sampling
## Not run: ML_MSBD(tree, initial_values = c(0.1, 10, 1), sigma = 1, time_mode = "mid") 
# Infer the most likely multi-states birth-death model with exponential decay 
# and full extant & extinct sampling
## Not run: ML_MSBD(tree, initial_values = c(0.1, 10, 0.5, 1), sigma = 1, 
  stepsize = 0.1, time_mode = "mid")
## End(Not run)