Fit a genealogical placement GMRF model using maximum likelihood

Fits the COD GMRF model using maximum likelihood. Additional arguments are passed to `optim`. If tau is not provided, `codls` is also used to optimise this parameter. This method is slower than `codls` and is not recommended for trees with more than several hundred samples.

Usage

codml(tr1, logtau = NULL, profcontrol = list(), ...)

Arguments

tr1

Phylogenetic tree in ape::phylo format

logtau

Precision parameter. If NULL, will invoke `tauprofile` to find best value.

profcontrol

Optional list of arguments passed to `tauprofile`

...

Additional arguments are passed to `mgcv::gam`

Value

A COD GMRF model fit. Includes the GAM model fit.

Details

The ML COD GMRF method does not currently support inverse probability weighting of samples. Use `codls` if sample weighting is needed.