outbreaker (version 1.1-8)

plotChains: Plot outbreaker's results

Description

These are the main functions used for generating graphics from the raw output of outbreaker and outbreaker.parallel.

Usage

plotChains(x, what = "post", type = c("series", "density"), burnin = 0,
  dens.all = TRUE, col = funky(x$n.runs), lty = 1, lwd = 1,
  main = what, legend = TRUE, posi = "bottomleft", ...)
transGraph(x, labels = NULL, burnin = x$burnin, threshold = 0.2,
  col.pal = NULL, curved.edges = TRUE, annot = c("dist", "support"),
  sep = "/", ...)
plotOutbreak(x, burnin = x$burnin, thres.hide = 0.2, col = NULL,
  col.pal = colorRampPalette(c("blue", "lightgrey")), edge.col.pal = NULL,
  col.edge.by = "prob", annot = c("dist", "prob"), sep = "/",
  cex.bubble = 1, edge.max.dist = 10, lwd.arrow = 2, xlim = NULL, ...)

Arguments

x

the output of outbreaker or outbreaker.parallel.

what

a character chains giving the name of the item to be plotted. See names(x$chains) for possible values. By default, log-posterior values are plotted

type

a character indicating if the chains should be plotted as time series ("series"), or as density ("density").

burnin

an integer indicating the number of MCMC steps to discard before plotting chains.

dens.all

a logical indicating if, in the case of multiple runs, the overall density of the different chains should be plotted in addition to individual densities.

col

a vector of colors to be used to plot different chains.

lty

a vector of integers specifying line types for the different chains.

lwd

same as lty, but for line width.

main

the title to be added to the plot.

legend

a logical indicating if a legend should be plotted for the different runs.

posi

a character string indicating the position of the legend (see ?legend).

…

further arguments to be passed to other functions.

labels

the labels to be used to name the nodes of the graph (cases).

threshold

the minimum support for ancestries to be plotted; 'support' is defined as the frequency of a given ancestor in the posterior distribution; defaults to 0.2.

col.pal, edge.col.pal

the color palette to be used for the edges (ancestries).

curved.edges

a logical indicating whether edges should be curved.

annot

a character indicating which information should be used to annotate the edges; this can be the distances between ancestors and descendents ("dist") and the posterior support for ancestries ("support"); if both are requested, fields will be concatenated.

sep

a character indicating the separator to be used when concatenating several types of annotation.

thres.hide

a threshold of posterior support for displaying ancestries; ancestries with less than this frequency in the posterior are hidden.

col.edge.by

a character string indicating which information should be used to color the edges ('dist': genetic distance; 'prob': support for the ancestry)

cex.bubble

a numeric value indicating the size factor for the bubbles representing the generation time distribution.

edge.max.dist

a number indicating the threshold distance bounding the color palette used for the edges; useful to avoid showing edges corresponding to distances larger than a given number.

lwd.arrow

a numeric value indicating the size factor for the arrows.

xlim

the limits of the X axis; if NULL, determined from the data.

Details

• plotChains is used for plotting MCMCs

• transGraph plots a graph of inferred ancestries

• plotOutbreak attempts to synthetize the reconstruction of small outbreaks

Examples

# NOT RUN {
data(fakeOutbreak)
attach(fakeOutbreak)

## examine MCMC
plotChains(res)
plotChains(res,type="dens")
plotChains(res,type="dens", what="mu1", burnin=2e4)

## represent posterior ancestries
transGraph(res, annot="", main="Posterior ancestries")
transGraph(res, annot="", main="Posterior ancestries - support > 0.5",
   threshold=0.5)
if(require(adegenet)){
transGraph(res, annot="", main="Posterior ancestries - support > 0.01",
   threshold=0.01, col.pal=spectral)
}
## summary plot
plotOutbreak(res,cex.bubble=0.5, thres.hide=0.5,
   main="Outbreak reconstruction")


detach(fakeOutbreak)


# }