OutbreakTools (version 0.1-16)

HorseFlu: Dataset from the Newmarket 2003 equine influenza outbreak

Description

This dataset is an obkData object with the following components:

• individuals: a dataframe which contains all static information relating to a horse (individualID), training yard the horse belongs to (yardID), date of birth, sex, latitude, longitude.

• dna: an '>obkSequences object containing DNA sequences and their meta-information.

• records: a list of dataframes containing information about the dates of first and last vaccinations, and shedding data (viral copy number) for some samples.

References

Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, et al. (2012) Transmission of Equine Influenza Virus during an Outbreak Is Characterized by Frequent Mixed Infections and Loose Transmission Bottlenecks. PLoS Pathog 8(12): e1003081. doi:10.1371/journal.ppat.1003081

Examples

# NOT RUN {
## LOAD DATA ##
data(HorseFlu)

## EXAMINE CONTENT ##
summary(HorseFlu)

## individual info
head(HorseFlu@individuals)

## DNA sequences
HorseFlu@dna

## records info
lapply(HorseFlu@records, head)


## How many individuals and sequences?
get.nindividuals(HorseFlu)
get.nsequences(HorseFlu)

## How many sequences per individual?
ind <- table(get.data(HorseFlu, "individualID", where="dna"))
ind
barplot(sort(ind), horiz=TRUE, las=1,
       xlab="number of samples", cex.names=.8)

## How many sequences for this individual?
ind.42 <- subset(HorseFlu, individualID="42")
get.nsequences(ind.42)

## How many samples?
length(unique(get.data(HorseFlu, "sampleID", where="dna")))

## How many sequences per sample?
table(get.data(HorseFlu, "sampleID", where="dna"))


# }