FluH1N1pdm2009: Dataset from the 2009 influenza A/H1N1 pandemic

In OutbreakTools: Basic Tools for the Analysis of Disease Outbreaks

Description

This dataset is a list containing the following objects:

1. individuals: a data frame containing 514 individual IDs as well as their locations.

2. samples: a data frame containing 514 individual IDs, their sample IDs and dates as well as the IDs of the associated genetic sequences.

3. dna: a DNAbin object containing 514 genetic sequences of influenza A/H1N1/2009 haemagglutinin (HA).

4. tree: a multiphylo object containing the maximum posterior probability tree obtained via the Beast analysis of the 514 genetic sequences.

Author(s)

Anton Camacho

References

This dataset is part of Trevor Bedford's tutorial on the Beast software: Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data, available at https://github.com/trvrb/influenza-dynamics-practical. In particular, the maximum posterior probability tree is taken from the sampled trees available at: https://github.com/trvrb/dynamics-practical/blob/master/output/pandemic_geo.trees.

Examples

## load the dataset
data(FluH1N1pdm2009)
attach(FluH1N1pdm2009)

head(individuals)
head(samples)


## create obkData object
x <- new("obkData", individuals = individuals, dna = FluH1N1pdm2009$dna,
      dna.individualID = samples$individualID, dna.date = samples$date,
      trees = FluH1N1pdm2009$trees)

## have a look at the summary
summary(x)

## plot the phylogeny
plotggphy(x, tip.color="location")

p <- plotggphy(x, ladderize = TRUE, branch.unit = "year")
p

detach(FluH1N1pdm2009)

OutbreakTools documentation built on Oct. 6, 2017, 1:03 a.m.