Description Author(s) Examples
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.
Anne Cori, Lulla Opatowski
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## 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')
## End(Not run)
|
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