Analysis of Outbreaks with Sequence Data

Implementation the outbreak analysis method described by Klinkenberg et al (2017) . Simulate outbreaks, analyse datasets by creating samples from the posterior distribution with a Markov-Chain Monte Carlo sampler, and summarize the output.


Outbreak reconstruction with sequence data

The package implements the method described in Klinkenberg et al (2016), doi: http://dx.doi.org/10.1101/069195

Workflow:

  • enter data and priors by constructing an object of S3-class 'phybreak', with function 'phybreak'

  • do mcmc-updates with functions 'burnin.phybreak' and 'sample.phybreak'; remove samples with 'thin.phybreak'

  • access the 'phybreak'-object by get.phybreak-functions such as 'get.tree', 'get.seqdata', 'get.parameters'

  • summarize the mcmc-chain with the functions 'transtree', 'infectorsets', 'phylotree', 'get.mcmc', 'get.phylo'

  • it is possible to simulate data with 'sim.phybreak'

News

phybreak 0.2.0

Major changes

  • Datasets added
  • Vignette phybreak_intro added
  • Use more samples per host, with changes in data input, the phybreak object structure, and plotting
  • Added mcmc-update steps for only the within-host phylogenetic minitree topology (not used by default)
  • Added transmission tree plotting function plotTrans
  • Data entry through new S3-class phybreakdata
  • Simulation with sim.phybreak results in phybreakdata-object, that can directly be plotted
  • MCMC progress shown on screen (10 sec intervals)

Minor changes

  • Faster simulation and phybreak construction with long sequences.
  • Automatic calculation of initial value for mu
  • Reference date in phybreak object (d-slot) referring to t = 0, used for transtree and plot
  • Minor changes in get.phybreak functions

BUG FIXES

  • Fixed bug in transtree with Edmonds method (index case could have been incorrect)
  • Correct on-screen log-likelihood during MCMC
  • Bug in sim.phybreak giving error with option output.class = "obkData"

phybreak 0.1.1

BUG FIXES

  • Solves issue with irreconcilable MCC trees in phylo-class vs table-form (#1) (reported by Mark Schultz)
  • Solves errors with OS X 10.9 Mavericks

Reference manual

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install.packages("phybreak")

0.2.0 by Don Klinkenberg, a year ago


Browse source code at https://github.com/cran/phybreak


Authors: Don Klinkenberg [aut, cre]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports Rcpp, methods, stats, stringr, utils

Depends on phangorn, ape

Suggests coda, phytools, OutbreakTools, testthat, knitr, rmarkdown

Linking to Rcpp


See at CRAN