MrBayes: Calls MrBayes

In shipunov: Miscellaneous Functions from Alexey Shipunov

Calls MrBayes

Description

A slight improvement of 'ips::mrbayes()'

Usage

MrBayes(x, file="", nst=6, rates="invgamma", ngammacat=4, nruns=2, ngen=1e+06,
 printfreq=100, samplefreq=10, nchains=4, savebrlens="yes", temp=0.2, burnin=10,
 contype="allcompat", run=FALSE, simple=TRUE, exec="mb-mpi", method="dna")

Arguments

x	The object to process (must be 'DNAbin' class)
file	A character string, giving the name of the MrBayes input file
nst	An integer giving the number of rates in the model of sequence evolution
rates	A character string; allowed are "equal", "gamma", "propinv", "invgamma", and "adgamma"; the default is "equal"
ngammacat	An integer; the number rate categories for the discretized Gamma distribution; the default is '4'
nruns	An integer; the number of runs
ngen	An integer; the number of states of the MCMC
printfreq	An integer; the interval between states of the MCMC to be printed on the screen
samplefreq	An integer; the interval between states of the MCMC to be sampled
nchains	An integer; number of Metropolis coupled MCMCs in each run
savebrlens	Logical; shall branch lengths be saved
temp	Heating parameter
burnin	An integer; the number of samples from the MCMC to be discarded prior to further analysis
contype	A character string; the type of consensus tree calculated from the posterior distribution of trees

either "halfcompat" (majority-rule consensus tree) or "allcombat" (strict consensus tree)

run	Logical; 'run = FALSE' will only print the NEXUS file, 'run = TRUE' will also start the MCMC runs, if the 'path' argument is correctly specified
simple	New option: if TRUE (default), then outputs tree in the format readable by functions from 'ape' package
exec	New option: name of UNIX executable (to allow multi-threaded version)
method	New option: either "dna", or "mixed" to handle mixed or purely morphologic data (see below)

Details

MrBayes() is an improvement of ips::mrbayes() and ips::mrbayes.mixed(). Please see its documentation for clarity and other options.

Comparing with 'ips' sources, MrBayes() has some code alterations and three more options. It also both views and saves output (works only on UNIX).

If 'method="mixed"', the function requires character matrix as input where missing data are labeled with "N", morphological columns encoded as 0/1 and placed after nucleotide columns (which might be absent).

Author(s)

Alexey Shipunov

See Also

ips::mrbayes

Examples

require(ips)
data(ips.cox1)
x <- ips.cox1[, 100:140]

## Not run: 
## requires MrBayes program installation
MrBayes(x, file="cox1", ngen=100, run=TRUE)

str(plantago)
plantago[is.na(plantago)] <- "N"
row.names(plantago) <- gsub(" ", "_", row.names(plantago))
## requires MrBayes program installation
tr <- MrBayes(plantago, file="plantago", method="mixed", burnin=5000, run=TRUE) # makes many files
tr <- tr[[1]]
tr <- root(tr, outgroup="Plantago_maritima", resolve.root=TRUE)
tr$node.label <- suppressWarnings(round(as.numeric(tr$node.label)*100)) # warning is OK
tr$node.label[tr$node.label == "NA"] <- ""
plot(tr)
nodelabels(tr$node.label, frame="none", bg="transparent", adj=-0.1)
add.scale.bar()

## End(Not run)

shipunov documentation built on Feb. 16, 2023, 9:05 p.m.