R interface for threshml


This function is an R interface for threshml in the PHYLIP package (Felsenstein 1989, 2013). threshml fits the threshold model of Felsenstein (2005; 2012). Note that threshml is new & not in the currently released version of PHYLIP (as of December 2013). It can be downloaded from its webpage here: http://evolution.gs.washington.edu/phylip/download/threshml/. If not specifying path, the executable file for threshml (e.g., threshml.exe in Windows) should be placed in the folder containing all other executable files for PHYLIP (e.g., C:/Program Files/phylip=3.695/exe in Windows).

Obviously, use of any of the functions of this package requires that PHYLIP (Felsenstein 2013) should first be installed. More information about installing PHYLIP can be found on the PHYLIP webpage: http://evolution.genetics.washington.edu/phylip.html.


Rthreshml(tree, X, types=NULL, path=NULL, ...)



object of class "phylo".


a data.frame of continuous valued or discrete character traits with rownames containing species names. Discrete & continuous characters can be supplied in any order. All discrete character traits must be two-state, but can be coded using any convention (i.e., 0, 1, "A","B", etc.).


character vector containing the types (e.g., "discrete", "continuous"). If types are not supplied, Rthreshml will try to figure out which columns via is.numeric.


path to the executable containing threshml. If path = NULL, the R will search several commonly used directories for the correct executable file.


optional arguments to be passed to threshml. See details for more information.


Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); burnin burnin generations for the MCMC; nchain number of chains of the MCMC; ngen number of generations in each chain; proposal variance on the proposal distribution for the MCMC; lrtest logical value indicating whether to conduct a likelihood-ratio test of the hypothesis that some correlations are zero (does not appear to work in the present version); and cleanup remove PHYLIP input/output files after the analysis is completed (defaults to cleanup = TRUE).


This function returns a list containing the results from threshml.


Liam J. Revell, Scott A. Chamberlain

Maintainer: Liam J. Revell <liam.revell@umb.edu>


Felsenstein, J. (1989) PHYLIP–Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.

Felsenstein, J. (2005) Using the quantitative genetic threshold model for inferences between and within species Philosophical Transactions of the Royal Society London B, 360, 1427-1434.

Felsenstein, J. (2012) A comparative method for both discrete and continuous characters using the threshold model. American Naturalist, 179, 145-156.

Felsenstein, J. (2013) PHYLIP (Phylogeny Inference Package) version 3.695. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

See Also


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