Phylogenetic Monte Carlo

Monte Carlo based model choice for applied phylogenetics of continuous traits. Method described in Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. doi:10.1111/j.1558-5646.2011.01574.x.


Beta, use with caution!

This is a lightweight implementation of my pmc package focusing on what I think are the more common use cases (e.g. it will no longer support comparisons of a geiger model against an ouch model). Further, it does not cover many of the newer model fitting that have been implemented since pmc was first released.

The goal of this release is mostly to provide compatibility with current versions of geiger.

Install the package:

library("devtools")
install_github("cboettig/pmc2")

A trivial example with data simulated from the lambda model.

library("pmc")
library("geiger")
phy <- sim.bdtree(n=10)
dat <- sim.char(rescale(phy, "lambda", .5), 1)[,1,]
out <- pmc(phy, dat, "BM", "lambda", nboot = 50)

Plot the results:

dists <- data.frame(null = out$null, test = out$test)
library("ggplot2")
library("tidyr")
library("dplyr")
## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
dists %>% 
  gather(dist, value) %>%
  ggplot(aes(value, fill = dist)) + 
  geom_density(alpha = 0.5) + 
  geom_vline(xintercept = out$lr)

Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. http://doi.org/10.1111/j.1558-5646.2011.01574.x

News

For a complete discription of changes see the Issues page on the package development site on GitHub.

  • Fixes bug introduced by new version of tidyr & dplyr
  • Fixes bug introduced by new version of tidyr
  • Completely re-written package compatible with current versions of geiger. May not be entirely backwards-compatible with previous versions of pmc. In particular, convenience functions for converting data formats between ape and ouch routines are no longer provided.
  • Updated vignette
  • Removed outdated COPYING file, see LICENSE
  • Allow cross comparisons between ouch-formatted & ape-formatted trees
  • Added error handling for cases when update routine fails
  • Fixed vignette
  • Fixed the "white" method, which was lacking the simulation routine necessary to run
  • License is now Creative Commons Zero (CC0).

Reference manual

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install.packages("pmc")

1.0.2 by Carl Boettiger, a year ago


https://github.com/cboettig/pmc


Report a bug at https://github.com/cboettig/pmc/issues


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


Authors: Carl Boettiger [aut, cre]


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


CC0 license


Imports dplyr, geiger, ggplot2, parallel, ouch, tidyr

Suggests covr, gridExtra, knitr, testthat


See at CRAN