P2C2M.Skyline

An R-package for assessing model adequacy for Bayesian Skyline Plots using posterior predictive simulation

##Installation:

P2C2M.Skyline can be installed from Github using the function install_github implemented in the devtools R-package.

library(devtools)
devtools::install_github("P2C2M/P2C2M_Skyline")

P2C2M.Skyline automatically installs all the dependencies, but if you get errors, try to install them individually. Here is the list of all required packages:

install.packages("ape")  
install.packages("phytools")  
install.packages("phyclust")
install.packages("pegas")  

Example:

To run P2C2M.Skyline, users need to provide an ultrametric phylogenetic tree (NEXUS format) and the log file resulting from a Bayesian Skyline analyzed in Tracer.

Rhinella granulosa – All samples

We included a Rhinella granulosa dataset in P2C2M.Skyline as an example. The Rhinella granulosa dataset includes 86 sequences of a mitochondrial fragment. So, we will investigate if the Skyline model is a good fit for the evolutionary history of Rhinella granulosa.

Users need to download and provide the path to ms software (Hudson, 2002).

library(P2C2M.Skyline)

P2C2M.Skyline(tree.file=system.file("extdata", "Rhinella_granulosa_tree_file.tre", package="P2C2M.Skyline"),
              log.file=system.file("extdata", "Rhinella_granulosa_log_file.txt", package="P2C2M.Skyline"),
              nrep=100,
              dir ="~/Desktop",
              path.to.ms = "~/Desktop/msdir/ms")

Analyzing all samples from the Rhinella granulosa dataset together represent a violation of the Skyline plot model (p-value < 0.05).

References:

Fonseca EM, Duckett JD, Almeida FG, Smith ML, Thomé TMC, Carstens BC. Assessing model adequacy for Bayesian Skyline Plots using posterior predictive simulation. In review

Hudson RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337–338. DOI: 10.1093/bioinformatics/18.2.337.