/working/auteur.extended/man/rjmcmc.bm.Rd

 1\name{rjmcmc.bm}
 2\alias{rjmcmc.bm}
 3\title{Bayesian sampling of trait evolutionary rates}
 4\description{Implements reversible-jump Markov chain Monte Carlo sampling to identify shifts in the process of continuous trait evolution across phylogenetic trees}
 5\usage{rjmcmc.bm(phy, dat, SE=0, ngen = 1000, sample.freq = 100, prob.mergesplit = 0.05, prob.root = 0.01, lambdaK = log(2), constrainK = FALSE, jumpsize = NULL, simplestart = FALSE, internal.only = FALSE, summary = TRUE, fileBase = "result")}
 6\arguments{
 7  \item{phy}{a phylogenetic tree of class 'phylo'}
 8  \item{dat}{a named vector of continuous trait values, associated with each species in \code{phy}; see \code{\link[geiger]{name.check}}}
 9  \item{SE}{a named vector of standard errors associated with each trait value; if a single value is given (e.g., \code{SE=0.05}), the standard error is assumed to apply for all trait values}
10  \item{ngen}{number of sampling generations}
11  \item{sample.freq}{frequency with which Markov samples are retained (e.g., \code{sample.freq=10} retains every tenth sample in the chain)}
12  \item{prob.mergesplit}{a value from 0 to 1, signifying the proportion of proposals that split rates or merge rates, thereby increasing or decreasing complexity of the evolutionary model}
13  \item{prob.root}{a value from 0 to 1, governing the proportion of proposals in which the root state is updated}
14  \item{lambdaK}{the shape parameter for the Poisson distribution used as a prior on the number of distinct rates in the tree (see \code{\link[stats]{rpois}})}
15  \item{constrainK}{if given an integer, Markov sampling becomes dimensionally constrained (e.g., \code{constrainK=2} would restrict posterior 
16  samples to be drawn only from models with two independent rates)}
17  \item{jumpsize}{if \code{NULL}, the proposal width is intialized through a calibration period (see \code{\link{calibrate.jumpsize}}); otherwise, 
18  proposal width is constrained to the supplied value}
19  \item{simplestart}{if \code{FALSE}, a random starting point (with \code{k} rate parameters) is chosen; if \code{TRUE}, Markov sampling begins under a global-rate model}
20  \item{internal.only}{a logical switch, dictating whether any branch in the tree can be chosen for a rate shift (\code{internal.only=FALSE}) 
21  or whether all but tips can be sampled for a rate shift}
22  \item{summary}{a logical switch that determines whether any output is printed to the console after the analysis has finished}
23  \item{fileBase}{a string used to uniquely identify the base directory to which Markov samples are written}
24}
25
26\details{
27In the two primary objects that store posterior estimates of \code{rate.shifts} and \code{rates} (see \bold{Value}), branches are labeled in accordance with the numeric identifiers found in \code{phy$edge}, which represents a table of ancestor-descendant
28 relationship (see \code{\link[ape]{read.tree}} and the first plot from the \bold{Examples} below).  In the \bold{Examples} below do \bold{not} expect convergence with such short chains!
29}
30\value{
31If \code{summary=TRUE} the global rate of acceptance and calibrated proposal width is returned as a list.  After a run has completed, the rates of acceptance for various proposal mechanisms are printed, along with 
32the calibrated jumpsize used for the last nine-tenths of the chain. 
33
34Posterior results are written to several files within a base directory, the contents of which are as follows:
35  \item{logfile}{a logfile including the following for each Markov sample; the generations at which samples were retained; the generalized model of trait evolution used for inference (e.g., Brownian motion or 'BM"); 
36  the mean treewide rate in the sampled generation; the number of independent rates; the root state; and the likelihood of the model at each sample.  Do not be alarmed if it seems to take some time before values 
37  begin to appear in the \code{logfile}: samples are not saved until after the calibration period has terminated }
38  \item{errors}{a logfile to which errors are recorded, if any are generated in the Markov chain}
39  \item{posteriorsamples}{a compressed .rda file, storing estimates from the Markov chain for relevant parameters; contents of this file can be loaded 
40  with \code{load("posteriorsamples.rda")}. This list object, whose referent is also \code{posteriorsamples} when in R-memory, includes two dataframes: 
41  \code{rates} comprises the relative-rate estimates for each branch in the phylogeny; \code{rate.shifts} stores the branches that were chosen for 
42  rate shifts in each retained sample of the Markov chain (\code{1} signifies a shift; 
43  \code{0} implies a branch that was not sampled for a rate shift). Column names of both components of \code{posteriorsamples} are from the numeric vector of 
44  branch labels (see \bold{Details}). For further information on .Rd and .rda files, see \code{\link[base]{save}} and \code{\link[base]{load}} as well as the 
45  \bold{Examples} below. }
46}
47
48\author{LJ Harmon, AL Hipp, and JM Eastman}
49\examples{
50#############
51## generate tree
52n=24
53phy=prunelastsplit(birthdeath.tree(b=1,d=0,taxa.stop=n+1))
54
55# plot phylogeny with branches labeled as they are identified in by rjmcmc.bm
56plot(phy, label.offset = strwidth(par("pch"), cex = 0.35)) ## PLOT ONE ##
57edgelabels(text=phy$edge[,2], frame="c", bg=add.transparency("white",0.75), cex=0.75)
58mtext("branch labels used by the reversible-jump sampler")
59
60#############
61## simulate a rate shift
62 # find an internal edge
63anc=get.desc.of.node(Ntip(phy)+1,phy)
64branches=phy$edge[,2]
65branches=branches[branches>Ntip(phy) & branches!=anc]
66branch=branches[sample(1:length(branches),1)]
67desc=get.descendants.of.node(branch,phy)
68rphy=phy
69rphy$edge.length[match(desc,phy$edge[,2])]=phy$edge.length[match(desc,phy$edge[,2])]*64
70e=numeric(nrow(phy$edge))
71e[match(c(branch,desc),phy$edge[,2])]=1
72cols=rev(diverge_hcl(n=2))
73dev.new()
74plot(phy,edge.col=ifelse(e==1,cols[1],cols[2]), edge.width=2) ## PLOT TWO ##
75mtext("expected pattern of rates")
76
77## simulate data on the 'rate-shifted' tree
78dat=rTraitCont(phy=rphy, model="BM", sigma=sqrt(0.1))
79
80## run two short reversible-jump Markov chains
81r=paste(sample(letters,9,replace=TRUE),collapse="")
82lapply(1:2, function(x) rjmcmc.bm(phy=phy, dat=dat, ngen=10000, sample.freq=10, prob.mergesplit=0.1, simplestart=TRUE, jumpsize=1, fileBase=paste(r,x,sep=".")))
83
84 # collect directories
85dirs=dir("./",pattern=paste("BM",r,sep="."))
86pool.rjmcmcsamples(base.dirs=dirs, lab=r)
87
88## view contents of .rda
89load(paste(paste(r,"combined.rjmcmc",sep="."),paste(r,"posteriorsamples.rda",sep="."),sep="/"))
90print(head(posteriorsamples$rates))
91print(head(posteriorsamples$rate.shifts))
92
93## plot Markov sampled rates
94dev.new()
95shifts.plot(phy=phy, base=paste(r,"combined.rjmcmc",sep="."), burnin=0.5, legend=TRUE, pdf=FALSE, edge.width=2) ## PLOT THREE ##
96
97## PASTE UNCOMMENTED FOLLOWING LINE TO DROP DIRECTORIES CREATED BY RJMCMC
98 # unlink(dir(pattern=paste(r)),recursive=TRUE)
99}