ctlMCMCtree: Generating the control file to run MCMCtree when using...

In dosreislab/mcmc3r: Tools to work with MCMCtree

Generating the control file to run MCMCtree when using morphological data

Description

Function that outputs the control file to run MCMCtree. It can be used to run only with morphological data or morphological+molecular data (more than one partition in the alignment file) together.

Usage

ctlMCMCtree(
  filename,
  mol = FALSE,
  seed = -1,
  seqfile,
  treefile,
  mcmcfile = "mcmc.txt",
  outfile = "out.txt",
  ndata,
  seqtype = 0,
  usedata = 1,
  clock,
  RootAge,
  TipDate,
  alpha,
  ncatG,
  cleandata = 0,
  BDparas,
  kappa_gamma,
  alpha_gamma,
  rgene_gamma,
  sigma2_gamma,
  print = 2,
  burnin,
  sampfreq,
  nsample,
  model
)

Arguments

filename	Character, name for the output control file.
mol	Boolean, TRUE if you include molecular data, FALSE otherwise. Default = FALSE.
seed	Numeric, seed value. Default = -1 (assigns random seed using computer's current time).
seqfile	Character, path to the alignment file.
treefile	Character, path to the tree file.
mcmcfile	Character, path to the file with the report of MCMC runs. By default it generates a file called "mcmc.txt" in the directory where MCMCtree is run.
outfile	Character, path to the summary results file. By default it generates a file called "out.txt" in the directory where MCMCtree is run.
ndata	Numeric, number of partitions in the alignment file.
seqtype	Numeric, 0 for nucleotide sequences, 1 for codon sequences, and 2 for amino acid sequences. Default = 0.
usedata	Numeric, 1: Calculate the likelihood function in the normal way, 0: Likelihood is not calculated (likelihood = 1), 2 and 3: approximate likelihood calculation and ML estimation of branch lengths (see details). Default = 1.
clock	Numeric, 1: strict clock model, 2: independent rates model, 3: autocorrelated rates model (see details).
RootAge	Character, calibration for the root.
TipDate	Numeric, time unit to scale the estimated divergence times. See details.
alpha	Numeric, alpha value for the discrete-gamma model of rate variation. Only used if molecular data is available.
ncatG	Numeric, number of categories for the discrete-gamma model of rate variation. Only used if molecular data is available.
cleandata	Numeric, 0: alignment gaps and ambiguity characters are treated as missing data, 1: any site where at least one sequences has an alignment gap or ambiguity character is deleted (see details). Default = 0.
BDparas	Numeric, vector with the parameters controlling the birth-death-sequential-sampling (BDSS) process (see details).
kappa_gamma	Numeric, vector with the parameters for the substitution model parameter kappa (transition/transversion rate ratio). Only used if molecular data is available.
alpha_gamma	Numeric, vector with the parameters for the substitution model parameter gamma (gamma shape parameter for variable rates among sites). Only used if molecular data is available.
rgene_gamma	Numeric, vector with the parameters for the Dirichlet-gamma prior for the mean substitution rate (see details).
sigma2_gamma	Numeric, vector with the parameters for the Dirichlet-gamma prior for the rate drift parameter (see details).
print	Numeric, 0: results are printed to screen only, 1: MCMC is written to "mcmcfile" and the summary to the "outfile", 2: same as 1 but rates for branches for each partitions are appended to "outfile". Default = 2.
burnin	Numeric, number of iterations to be discarded (burn-in).
sampfreq	Numeric, number of iterations after which a sample will be collected.
nsample	Numeric, number of samples to be gathered.
model	Numeric, substitution model to be used (see details). 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85, 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu. Only used if molecular data is available.

Details

For more information, please check the MCMCtree tutorial and the PAML documentation.

Examples

# First create objects with the path to alignment and tree files and then
# call the function to generate the control file. The parameters not passed
# to the function are used as the default values
tree <- system.file( "extdata", "19s.trees", package = "morpho")
aln  <- system.file( "extdata", "seqfile.aln", package = "morpho")

# Uncomment the following lines followed by "##" and change the path in the filename so
# it is saved where you want
##ctlMCMCtree( filename = "../mcmctree.ctl", mol = FALSE, seqfile = aln, treefile = tree,
##ndata = 1, clock = 2, TipDate = 1, RootAge = c("B(37.3, 66.0, 0.025, 0.025)"),
##BDparas = c( 1, 1, 0, 0.001 ), rgene_gamma = c( 2, 5 ),
##sigma2_gamma = c( 2, 2 ), burnin = 50000, sampfreq = 50, nsample = 20000 )

dosreislab/mcmc3r documentation built on March 29, 2024, 6:45 p.m.