print.outbreaker_chains {outbreaker2}R Documentation

Basic methods for processing outbreaker results

Description

Several methods are defined for instances of the class outbreaker_chains, returned by outbreaker, including: print, plot, summary

Usage

## S3 method for class 'outbreaker_chains'
print(x, n_row = 3, n_col = 8, ...)

## S3 method for class 'outbreaker_chains'
plot(
  x,
  y = "post",
  type = c("trace", "hist", "density", "alpha", "t_inf", "kappa", "network"),
  group = NULL,
  burnin = 0,
  min_support = 0.1,
  labels = NULL,
  ...
)

## S3 method for class 'outbreaker_chains'
summary(object, burnin = 0, method = c("mpa", "decycle"), ...)

Arguments

x

an outbreaker_chains object as returned by outbreaker.

n_row

the number of rows to display in head and tail; defaults to 3.

n_col

the number of columns to display; defaults to 8.

...

further arguments to be passed to other methods

y

a character string indicating which element of an outbreaker_chains object to plot

type

a character string indicating the kind of plot to be used (see details)

group

a vector of character strings indicating the parameters to display, or "all" to display all global parameters (non node-specific parameters).

burnin

the number of iterations to be discarded as burnin

min_support

a number between 0 and 1 indicating the minimum support of ancestries to be plotted; only used if 'type' is 'network'

labels

a vector of length N indicating the case labels (must be provided in the same order used for dates of symptom onset)

object

an outbreaker_chains object as returned by outbreaker.

method

the method used to determine consensus ancestries. 'mpa' (maximum posterior ancestry) simply returns the posterior ancestry with the highest posterior support for each case, even if this includes cycles. 'decycle' will return the maximum posterior ancestry, except when cycles are detected, in which case the link in the cycle with the lowest support is pruned and the tree recalculated.

Details

type indicates the type of graphic to plot:

Author(s)

Thibaut Jombart (thibautjombart@gmail.com)

See Also

See introduction vignette for detailed examples on how to visualise outbreaker_chains objects.


[Package outbreaker2 version 1.1.3 Index]