Added argument lr.penalty to functions mleLR() and mlePath()
allow penalization of the covariance matrix
on both the additive log-ratio and centered log-ratio scales.
Added argument lr to both logitNormalVariation() and naiveVariation()
to allow calculation of metrics of proportionality on either
the ALR or CLR scale.
Added function convertSigma() to allow easy conversion
between covariance matrices on ALR and CLR scales.
Function pluginVariation() is now deprecated as its results will
now be equivalent to naiveVariation().