This is a lightweight implementation of mypmc packagefocusing on what I think are the more common use cases (e.g. it will nolonger support comparisons of ageiger model against anouch model). Further, it does not cover many of the newermodel fitting that have been implemented sincepmc wasfirst released.
The goal of this release is mostly to provide compatibility withcurrent versions ofgeiger.
Install the package:
library("devtools")install_github("cboettig/pmc")A trivial example with data simulated from thelambdamodel.
library("pmc")library("geiger")#> Loading required package: ape#> Loading required package: phytools#> Loading required package: mapslibrary("phytools")phy<-sim.bdtree(n=10)dat<-sim.char(rescale(phy,"lambda", .5),1)[,1,]out<-pmc(phy, dat,"BM","lambda",nboot =50)#> Warning in geiger::fitContinuous(phy = tree, dat = data, model = model, :#> Parameter estimates appear at bounds:#> lambdaPlot 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:ape':#>#> where#> 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 phylogenyinformative? Measuring the power of comparative methods, Evolution 66(7) 2240-51.https://doi.org/10.1111/j.1558-5646.2011.01574.x