OutbreakTools (version 0.1-16)

Plot obkData: Plot outbreak data

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 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).

See Also

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

Examples

# NOT RUN {
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")
# }