Description Author(s) Examples
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$individuals
, a data.frame
containing:
the ID of each individual, stored in the row names of the data.frame
infector
, the ID of the infector of each individual
DateInfected
, the date at which each individual was infected
Sex
, the sex of each individual
Age
, the age of each individual
lat
, the latitute corresponding to each individual
lon
, the longitude corresponding to each individual
- ToyOutbreakRaw$records
, 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.
- ToyOutbreakRaw$contacts
, a matrix
with two columns
called from
and to
describing contacts between
individuals
- ToyOutbreakRaw$contacts.start
, a vector
containing the
start dates of each contact stored in ToyOutbreakRaw$contacts
.
- ToyOutbreakRaw$contacts.end
, a vector
containing the
end dates of each contact stored in ToyOutbreakRaw$contacts
.
- ToyOutbreakRaw$dna
is a list of two DNAbin
matrices
corresponding to two different genes.
- ToyOutbreakRaw$dna.info
is a data.frame containing:
individualID
, the ID of individuals for each sequence.
sampleID
, an indicator of samples from which sequences
were obtained.
date
, the date at samples were collected.
- ToyOutbreakRaw$tree
is a multiphylo
object storing a
phylogenetic tree.
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 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | ## 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'),zoom=13,colorBy='Sex')
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.