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().