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All other likelihoods commonly used for composition data share at least one of these weaknesses but there is one – the logistic-normal – which can be extended to avoid both.
The generalized PLS method presented could easily be applied to other likelihoods as well.
Our method also easily generalizes to other likelihoods than the Cox proportional hazards likelihood.
The R-INLA code is also included to give a good starting point to users who wants to make modifications, e.g., other likelihoods or more random effects.
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The prediction errors for RZWQM2 outputs with CL function were relatively lower and uniform compared with other likelihood functions composed of individual calibration criterion.
These techniques can also be applied to other likelihood-based phylogeny software.
This latter estimator was shown to outperform other likelihood-based estimators (Ghosh et al. 2008; Faye et al. 2010).
The reason for using NEIGHBOR instead of other likelihood-based programs was speed and because Urec considers only tree topology.
The other likelihood for the polymerization of gold nanoparticles seems the occurrence of the Brownian motion of the biomass in the systems.
All other likelihood ratio tests comparing the among sites models, were not in favor of an ω value greater than one among sites (Table 5).
We briefly discuss the features that distinguish RAxML-Light from standard RAxML, other likelihood-based phylogeny programs, and the BEAGLE library (Ayres et al., 2011).
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