Find the maximum likelihood, using numerical optimization with optim.
fitCauchy.internal(
phy,
X,
y,
model = c("cauchy", "lambda"),
method = c("reml", "random.root", "fixed.root"),
starting.value = list(x0 = NULL, disp = NULL, lambda = NULL),
lower.bound = list(disp = 0, lambda = 0),
upper.bound = list(disp = Inf, lambda = 1),
root.edge = 100,
optim = c("local", "global"),
method.init.disp = "Qn",
...
)A list, with the maximum likelihood rate parameter, and the likelihood value.
a phylogenetic tree of class phylo.
a model for the trait evolution. One of "cauchy" or "lambda" (see Details).
the method used to fit the process.
One of reml (the default), fixed.root or random.root.
See Details.
starting value for the parameters of the Cauchy.
This should be a named list, with x0 and disp the root starting value and the dispersion parameter.
The default initial values are computed from standard statistics used on (independent) Cauchy variables, see Details.
named list with lower bound values for the parameters. See Details for the default values.
named list with upper bound values for the parameters. See Details for the default values.
multiplicative factor for the root dispersion, equal to the length of the root edge. Ignored if method!=random.root.
if "local", only a local optimization around the initial parameter values is performed (the default).
If "global", a global maximization is attempted using the "MLSL" approach (see nloptr).
the initialization method for the dispersion. One of "Qn", "Sn", "MAD", "IQR". Default to the "Qn" statistics. See Details.
Rothenberg T. J., Fisher F. M., Tilanus C. B. 1964. A Note on Estimation from a Cauchy Sample. Journal of the American Statistical Association. 59:460–463.
cauphylm