Internal function. Constructor to allow fixing of rate parameters.
make.likRatePhylo(rateData, fixed, common.mean = FALSE, lambda.est, meserr)
an object of class "rateData"
A vector stating whether each parameter should be allowed to vary (either FALSE
which results in a start value of 1, or a numeric start value) or should be fixed (TRUE
).
a logical specififying whether each rate category should have its own mean (common.mean=FALSE
) or all categories should have the same mean (common.mean=FALSE
). See Thomas et al. (2009) for a discussion on the impact of assumptions about mean on rate estimates..
Logical - Logical. Fit Pagel's lambda.
an object of class "rateData"
Returns a function to be passed to optim.likRatePhylo