Description Usage Arguments Value Author(s) References Examples
phybreakdata takes as data sequences and sampling times and makes a phybreakdata
object.
If no host names are provided, each sample is assumed to be associated with a separate host. The number of sequences
should be equal to the length of the sampling time vector, and the position identifies the host (unless named
vectors are provided). Sample names can be provided separately;
otherwise it will be tried to extract them from the sequences or sampling times.
It is also possible to include (otherwise unobserved) simulated data: sim.infection times, sim.infectors,
and a (phylogenetic) sim.tree. This is done automatically when using sim.phybreak
.
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sequences |
Sequence data of class |
sample.times |
A vector of sampling times ( |
spatial |
Either a distance matrix ( |
sample.names |
A vector with sample names. |
host.names |
A vector with host names. The vector identifies the host for each sample, so should be of the same
length as |
sim.infection.times |
A vector with infection times ( |
sim.infectors |
A vector with infectors, either by name or by position (use 0 for the index case). |
sim.tree |
A tree of class |
An object of class phybreakdata
with the following elements
a 'phyDat'
-object with the sequence data.
a named vector
with the sample times.
a named vector
with the hosts from whom the samples have been taken.
a named distance matrix (class dist
) with the mutual distances.
a named vector
with the (simulated) infection times (if provided).
a named vector
with the (simulated) infectors (if provided).
a 'phylo'
-object with the (simulated) phylogenetic tree (if provided).
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.
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