Description Author(s) References Examples
This dataset is a list
containing the following
objects:
individuals
: a data
frame containing 514 individual IDs as well as their
locations.
samples
: a data frame containing
514 individual IDs, their sample IDs and dates as well as
the IDs of the associated genetic sequences.
dna
: a DNAbin
object containing
514 genetic sequences of influenza A/H1N1/2009
haemagglutinin (HA).
tree
: a
multiphylo
object containing the maximum
posterior probability tree obtained via the Beast
analysis of the 514 genetic sequences.
Anton Camacho
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## 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)
|
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