OutbreakTools (version 0.1-13)

ToyOutbreakRaw: Raw simulated outbreak dataset

Description

This dataset is a fake dataset containing information on an outbreak amongst 418 individuals. It contains a list called ToyOutbreakRaw of the following objects:

- ToyOutbreakRaw$individuals, a data.frame containing:

• the ID of each individual, stored in the row names of thedata.frame

infector, the ID of the infector of each individual DateInfected, the date at which each individual was infected Sex, the sex of each individual Age, the age of each individual lat, the latitute corresponding to each individual lon, the longitude corresponding to each individual

code

multiphylo

itemize

• individualID, the ID of individuals for each sequence.

item

• date, the date at which temperature was measured in each individual,
• temperature, the temperature measured in each individual.
• sampleID, an indicator of samples from which sequences were obtained.
• date, the date at samples were collected.

Examples

## Load data ##
data(ToyOutbreakRaw)
attach(ToyOutbreakRaw)

## Constructing an obkData object ##
x <- new ("obkData", individuals=individuals, records=records,
          contacts=contacts, contacts.start=contacts.start,
          contacts.end=contacts.end, dna=dna,
          dna.individualID=dna.info$individualID,
          dna.date=dna.info$date, sample=dna.info$sample, trees=trees)

detach(ToyOutbreakRaw)


## Examining the object ##
summary(x)

head(x@individuals)
head(x@records)
names(x@records)
head(x@records$Fever)
x@contacts
x@dna
x@trees

## Plotting the dynamic contact network ##
par(mfrow=c(2,2))
plot(get.contacts(x),main="Contact network - days 0-3",displaylabels=TRUE)
plot(get.contacts(x, from=0, to=1.1), main="Contact network - days 0-1",
     displaylabels=TRUE)
plot(get.contacts(x, from=2, to=2.1), main="Contact network - day 2",
     displaylabels=TRUE)
plot(get.contacts(x, from=3, to=3.1), main="Contact network - day 3",
     displaylabels=TRUE)

## Mapping the outbreak (by sex) ##
plot(x,'geo',location=c('lon','lat'),isLonLat=TRUE,zoom=13,colorBy='Sex')