Description Usage Arguments Author(s)
Calculates the maximum likelihood estimate and the value of the likelihood at the MLE of a BiChroM and BiChroM reduced models
1 2 3 4 | bichrom_optim(phy.tree, tip.values, model = "bichrom",
model.args = list(size = 50), starting.val, root.dist,
optim.options = list(algorithm = "NLOPT_LN_SBPLX", ftol_rel = 1e-08,
print_level = 1, maxtime = 1.7e+08, maxeval = 1000))
|
phy.tree |
phylogenetic tree |
tip.values |
A vector with chromosome numbers and/or binary trait states. See Zenil-Ferguson et al 2017 supplement for an explanation of BichroM model. |
model |
options are "bichrom" or "reducedbichrom" |
model.args |
List of arguments passed in each specified model other than parameters like size (default size is 50 chromosomes) |
starting.val |
vector of parameters in log scale that help with the optimization of the likelihood |
root.dist |
vector of probabilities for the states at the root |
optim.options |
See opts from nloptr package, optimization options for the likelihood function |
Rosana Zenil-Ferguson
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