OutbreakTools (version 0.1-16)

ToyOutbreak: Simulated outbreak dataset

Description

This dataset is a fake dataset containing information on an outbreak amongst 418 individuals. It contains an obkData object called ToyOutbreak.

ToyOutbreak@individuals is a data.frame containing:

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

ToyOutbreak@records is a list containing one data.frame called Fever containing:

• individualID, the ID of each individual,

• date, the date at which temperature was measured in each individual,

• temperature, the temperature measured in each individual.

ToyOutbreak@contacts is an obkContacts object describing the contacts inferred from the first four days of the epidemic tree (it is inferred that a contact occurred between each case and his/her infector within the day preceding infection).

ToyOutbreak@dna is an obkSequences object storing simulated DNA sequences (for 2 genes, gene1 and gene2).

ToyOutbreak@tree is a multiphylo object storing one phylogenetic tree derived from the concatenated genes.

Examples

# NOT RUN {
## Load data ##
data(ToyOutbreak)

## Overview of the dataset ##
summary(ToyOutbreak)

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

# }
# NOT RUN {
## Mapping the outbreak (by sex) ##
plot(ToyOutbreak,'geo',location=c('lon','lat'), zoom=13,
     colorBy='Sex')
# }