infectorsets: Sampled infectors for each host in a phybreak-object.
In donkeyshot/phybreak: Analysis of Outbreaks with Sequence Data

Description Usage Arguments Value Author(s) References Examples

The function takes a phybreak-object containing MCMC-samples, and returns for each host the posterior infectors, with support per infector. That can be in the form of a list, with infectors ordered by support, or in the form of a matrix with supports for all host-infector combinations (host in columns, infectors in rows).

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infectorsets(x, which.hosts = "all", percentile = 0.95,
  minsupport = 0, samplesize = Inf, infector.name = TRUE,
  support = c("proportion", "count"), output = c("list", "matrix"))

`x`	An object of class `phybreak`.
`which.hosts`	A vector with hosts (exact names or positions in the dataset), or `"all"` for all hosts.
`percentile`	Return infectors ordered by support, until a cumulative support indicated by `percentile`, support measured by proportion (value between 0 and 1).
`minsupport`	Only return infectors with more support than `minsupport`. Values in the range [0,1) are interpreted as support in `"proportion"` of posterior samples, values >= 1 as `"count"` of posterior samples.
`samplesize`	The number of samples to include (taken from the tail of the MCMC-chain).
`infector.name`	Whether to return the names of the infectors, or their position in the dataset.
`support`	Whether to return the support (= posterior probability) for each infector as a `"proportion"` or as a `"count"` of posterior trees in which that transmission link or transmission cluster is present.
`output`	Whether to return a `list` of hosts with infectors, or a `matrix` with support values for all host-infector pairs. Arguments `percentile`, `samplesize`, and `infector.name` are not used in case of `matrix`.

A named list with data.frames, each with a vector of infectors and a vector of supports. Or a matrix with supports for each host-infector pair.

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.

#First build a phybreak-object containing samples.
simulation <- sim_phybreak(obsize = 5)
MCMCstate <- phybreak(dataset = simulation)
MCMCstate <- burnin_phybreak(MCMCstate, ncycles = 20)
MCMCstate <- sample_phybreak(MCMCstate, nsample = 50, thin = 2)

infectorsets(MCMCstate)