R/datasets.R

In phylodyn: Statistical Tools for Phylodynamics

#' New York Influenza Genealogy
#' 
#' This dataset is a \code{phylo} object of a genealogy generated by BEAST from
#' the sequence data in Rambaut, et al. 2008.
#' 
#' A. Rambaut, O. G. Pybus, M. I. Nelson, C. Viboud, J. K. Taubenberger, E. C. 
#' Holmes The genomic and epidemiological dynamics of human influenza A virus. 
#' Nature, 453(7195): 615-619, 2008.
"NY_flu"

#' Regional Influenza Genealogy
#' 
#' This dataset is a \code{phylo} object of a genealogy generated by BEAST from
#' the sequence data in Zinder, et al. 2014.
#' 
#' D. Zinder, T. Bedford, E. B. Baskerville, R. J. Woods, M. Roy, M. Pascual.
#' Seasonality in the migration and establishment of H3N2 Influenza lineages
#' with epidemic growth and decline. BMC Evolutionary Biology, 14(1): 272, 2014.
"regional_flu"

#' Bottle_20c
#' 
#' This dataset is a \code{multiPhylo} object of 1435 coalescent trees of 20 individuals simulated under the SMC' process. This dataset was generted with macs  using the following command: \code{./macs20 300000 -t 4.0 -eN 0 1 -eN 0.3 0.1 -eN 0.5 1 -T -r .002 -h 1 (SEED: 1420826310)} 
"Bottle_20c"