Usage
jmodeltest(x, sub.schemes = 3, unequal.base.freq = FALSE,
prop.inv.sites = FALSE, rate.var = NULL, AIC = FALSE, AICc = FALSE,
BIC = FALSE, DT = FALSE, param.imp = FALSE, model.average = FALSE,
numThreads = 1, path = ifelse(.Platform$OS.type == "windows",
"C:/Program Files/jModelTest", "/usr/local/bin/jmodeltest"),
java.opts = NULL)
Arguments
x
a list of DNA sequences.
sub.schemes
number of substitution schemes to test. Can be one
of 3, 5, 7, 11, or 203.
unequal.base.freq
logical. Include models with unequal base
frequencies?
prop.inv.sites
logical. Include models with a proportion of
invariable sites?
rate.var
number of categories for models with rate variation
among sites.
AIC, AICc, BIC, DT
logical. Calculate respective information
criterion metrics?
param.imp
logical. Calculate parameter importances?
model.average
logical. Do model averaging and parameter importances?
numThreads
Number of threads to use.
path
path where jModelTest.jar is located.
java.opts
options to java command line.