This vignette shows a case study of New York influenza data, using
We start by loading the
In preparation, we aligned the sequences using the software MUSCLE,
and inferred a maximum clade credibility genealogy using the software BEAST[^1].
We packaged this genealogy in a
NY_flu, and we load it now.
[^1]: We infer the genealogy branch lengths in units of years using a strict molecular clock, a constant effective population size prior, and an HKY substitution model with the first two nucleotides of a codon sharing the same estimated transition matrix, while the third nucleotide's transition matrix is estimated separately.
We use BNPR and BNPR_PS to calculate approximate marginals (without and with a sampling model).
NY_cond = BNPR(data = NY_flu, lengthout = 100) NY_pref = BNPR_PS(data = NY_flu, lengthout = 100)
We plot the results (we use a scaling factor because we stored the object with units of weeks, and we standardize on units of years).
axlabs = list(x = seq(0, 12*52, by=52) + 10, labs = seq(2005, 1993, by=-1)) par(mfrow=c(1,3), cex=0.9, cex.lab=1.5, cex.main=1.7, oma=c(2.5, 2, 0, 0)+0.1, mar=c(2,1.5,2,1), mgp = c(2.5,1,0), xpd=NA, fig=c(0, 0.32, 0, 1)) plot_BNPR(NY_cond, main="BNPR", ylim = c(10, 500)/52, yscale = 1/52, col = rgb(0.829, 0.680, 0.306), axlabs = axlabs, heatmap_labels_side = "left") par(fig=c(0.32, 0.64, 0, 1), new=TRUE) plot_BNPR(NY_pref, main="BNPR-PS", ylim = c(10, 500)/52, yscale = 1/52, ylab = "", col = rgb(0.330, 0.484, 0.828), axlabs = axlabs, heatmap_labels = FALSE) par(mar=c(2,3.5,2,1), fig=c(0.64, 1.0, 0, 1), new=TRUE) plot_mrw(list(NY_cond, NY_pref), axlabs = axlabs, ylab = "Mean Relative Width", cols = c(rgb(0.829, 0.680, 0.306), rgb(0.330, 0.484, 0.828)), legends = c("BNPR", "BNPR-PS"), legend_place = "topright", legend_cex = 0.8)
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A. J. Drummond, M. A. Suchard, D. Xie, and A. Rambaut. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29:1969–1973, 2012.
A. Rambaut, O. G. Pybus, M. I. Nelson, C. Viboud, J. K. Taubenberger, and E. C. Holmes. The genomic and epidemiological dynamics of human influenza A virus. Nature, 453 (7195):615–619, 2008.
M. D. Karcher, J. A. Palacios, T. Bedford, M. A. Suchard, and V. N. Minin. Quantifying and mitigating the effect of preferential sampling on phylodynamic inference. arXiv preprint arXiv:1510.00775, 2015.
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