obkDataPlot: Plot outbreak data

In OutbreakTools: Basic Tools for the Analysis of Disease Outbreaks

Description

The plot method of obkData objects includes various options:

• timeline: plots requested information as time series; uses plotIndividualTimeline.

• geo: plots requested information as geographic distribution, on a map; uses plotGeo.

• mst: minimum-spanning tree based on genetic distances; uses plotggMST.

• phylo: plot phylogenetic trees stored in the object; uses plotggphy.

• contacts: plot contacts between individuals stored in the object; uses plot.obkContacts.

Usage

## S4 method for signature 'obkData'
plot(x, y=c("timeline","geo","mst","phylo","contacts"), ...)

Arguments

x	a obkData object
y	a character indicating the type of plot to be generated; can be "timeline" (default), "geo", "mst", "phylo", or "contacts".
...	further arguments to be passed to the plotting function, depending on the type of plot selected (see description above).

Author(s)

Rolf Ypma [e-mail], Thibaut Jombart [e-mail]

See Also

plotIndividualTimeline, plotGeo, plotggMST, plotggphy, plot.obkContacts.

Examples

data(HorseFlu)
head(HorseFlu)

## default plot: time line
plot(HorseFlu,orderBy='yardID',colorBy='yardID')
plot(HorseFlu,orderBy='yardID',colorBy='yardID',
     selection=1:30) # only the first 30

## plot contacts
data(ToyOutbreak)
plot(ToyOutbreak, "contacts")

## Not run: 
## plot geographic distribution of individuals
plot(HorseFlu, "geo", location=c('lon','lat'), colorBy='sex',
     zoom=12,center='9')

## plot minimum spanning tree for first 10 individuals
get.nindividuals(HorseFlu)
plot(subset(HorseFlu, individuals=1:10), "mst")

## End(Not run)

OutbreakTools documentation built on Oct. 6, 2017, 1:03 a.m.