Fitting puncutated and gradual evolutionary models in R

Installation

The pulsR package is installed using devtools:

# install the devtools package (if needed)
install.packages("devtools")

# load the devtools library
library(devtools)

# install the pulsR package
install_github("https://github.com/Schraiber/pulsR")

Library

Once installed, pulsR is loaded like other R packages:

# load the pulsR library
library(pulsR)

Data format

Phylogenies are expected to be in ape format. Data are expected to be in a named vector, in which names correspond to tips of the phylogeny.

Example data

Vertebrate data used in Landis and Schraiber (2017) can be found in vertebrate.body_size.clean.rds

Fitting data

Data can be fit using the function fit_reml_levy in the levy_pruning_optim.r script. The main parameters are phy, which is an ape format phylogeny; dat, which is a named vector of measurements; and model, which indicates which model to fit. Possible models are BM, OU, JN, VG, NIG, BMJN, BMVG, and BMNIG. Additional paremeters are described in the script file.

This function returns a list with an element params indicating the maximum likelihood parameters. Other returned elements are explained in the script file.

Simulating data

Data can be simulated using the function rlevy in levy_prurning_sim.r. Simulation requires an ape format phylogeny and a model (same choices as above). Models require parameters; for explanation of parameters, see Landis and Schraiber (2017).