In our description of the model, the alternative scenarios based on CRM, ARM, and FAM are considered on equal footing.
But a single payer model, the alternative, is also incapable of optimizing quality and efficiency in the short term.
In the AHP model, the alternative selection problem is structured into a hierarchy, with the overall goal placed at the top, with lower-level selection criteria below.
First we conducted the 'branch' test [ 53, 54, 59, 60] where model 2 (the alternative model) is compared to model 0 (null model).
M7 and M8a models are the null models without positive selection (no codon with Ka/Ks > 1) and the M8 model is the alternative model with positive selection.
The significance of difference between the null model and the alternative model was evaluated by calculating twice the log-likelihood difference following a χ2 distribution, with the number of degrees of freedom.
We conducted an LRT between the null model and the alternative model for each gene.
The LRT compares the log-likelihoods of a null model with the alternative model.
The test statistic for the LRT is calculated as twice the difference between the likelihood scores of the null model and the alternative model.
For both the null model and the alternative model, beta distribution parameters (α and β) were estimated via a maximum likelihood approach, using the R function optim.
