Learn R Programming
⚠️There's a newer version (1.0.6) of this package.Take me there.

pmc (version 0.0-8)

Phylogenetic Monte Carlo

Description

Monte Carlo based model choice for applied phylogenetics of continuous traits

Copy Link

Version

Install

install.packages('pmc')

Monthly Downloads

307

Version

0.0-8

License

CC0

Issues

3

Pull Requests

0

Stars

2

Forks

1

Maintainer

Carl Boettiger

Last Published

March 4th, 2013

Functions in pmc (0.0-8)

getParameters.browntree

Method to extract the parameters
convert

toggles between ouch and ape format trees
loglik.fitContinuous

Method to extract the log likelihood
anoles

The anoles data set
get_data.fitContinuous

Method to grab the data
loglik.browntree

Method to extract the log likelihood
loglik

S3 generic to provide a log-likelihood
get_phy.fitContinuous

Method to grab the phylogeny
getParameters.hansentree

Method to extract the parameters
tree

The phylogeny for the anoles data set
paintBranches

Paints branches with regimes changing at nodes specified
treepower

function to create the power curve for a tree
get_data

S3 generic to grab trait data
plot_pars

plot the parameter distributions
treepalette

flexible regime coloring for trees
mrcaOUCH

Finds the most recent common ancestor on an OUCH formatted tree
simulate.fitContinuous

simulate method
loglik.hansentree

Method to extract the log likelihood
get_phy.ouchtree

Method to grab the phylogeny
getParameters

S3 generic to provide the parameters
pmc_fit

Fit any model used in PMC
get_phy

S3 generic to extract the phylogeny
plot.pmc

plot the distributions
simulate_and_update

Internal helper function Simulates under model A, updates both A and B based on that data
getParameters.fitContinuous

Method to extract the parameters
format_data

format data in ape format into ouch format
get_data.ouchtree

Method to grab the data
compute_regimes

internal method for computing the regimes used by format_data()
matchformats

Internal helper function to match data formats
update.fitContinuous

update a fitContinuous model
fitContinuous_object

wrapper for fitContinuous
pmc

Performs a phylogenetic monte carlo between modelA and modelB