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.
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
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
Install the package:
A trivial example with data simulated from the
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 object is masked from 'package:ggplot2':#>#> vars#> The following objects are masked from 'package:stats':#>#> filter, lag#> The following objects are masked from 'package:base':#>#> intersect, setdiff, setequal, uniondists %>%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
For a complete discription of changes see the Issues page on the package development site on GitHub.
fix CITATION file to use as.person() compatible author list fix images in README