Description Usage Arguments Details Value Author(s) References Examples
View source: R/logLik-phybreak.R
The likelihood of a phybreak
-object is calculated, with the option to include or exclude parts of the
likelihood for genetic data, phylogenetic tree (within-host model), sampling times and generation times.
1 2 3 |
object |
An object of class |
genetic |
Whether to include the likelihood of the mutation model. |
withinhost |
Whether to include the likelihood of within-host (coalescent) model. |
sampling |
Whether to include the likelihood of the sampling model (sampling intervals). |
generation |
Whether to include the likelihood of the transmission model (generation intervals). |
... |
Some methods for this generic require additional arguments. None are used in this method. |
The sequence likelihood is calculated by Felsenstein's pruning algorithm, assuming a prior probability of 0.25 for each nucleotide. The within-host likelihood is the likelihood of coalescence times given the within-host model and slope. The generation interval and sampling interval likelihood are log-densities of the gamma distributions for these variables.
The log-likelihood as an object of class logLik.
Don Klinkenberg don@xs4all.nl
Klinkenberg et al. (2017) Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput Biol, 13(5): e1005495.
1 2 3 4 5 6 7 8 9 10 11 12 13 | #First build a phybreak-object containing samples.
simulation <- sim.phybreak(obsize = 5)
MCMCstate <- phybreak(data = simulation)
logLik(MCMCstate)
MCMCstate <- burnin.phybreak(MCMCstate, ncycles = 20)
logLik(MCMCstate)
tree0 <- get.phylo(MCMCstate)
seqdata <- get.seqdata(MCMCstate)
pml(tree0, seqdata, rate = 0.75*get.parameters(MCMCstate)["mu"])
logLik(MCMCstate, genetic = TRUE, withinhost = FALSE,
sampling = FALSE, generation = FALSE) #should give the same result as 'pml'
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