The likelihood was evaluated over a two-dimensional grid of values of sensitivity, S, and of inverse of MST, λ.
The likelihood was evaluated at scheduled time points (typically once per week) and at state changes on nonscheduled days Effects of time, drug exposure, receptor occupancy, and covariates on transition probabilities were evaluated in the Markov model as a proportional relation on the transition rate parameters.
In winner-takes-all, after the clean speech is imputed for each Gaussian belonging to state s, the mixture's likelihood is evaluated for all imputed values and the most likely imputation is selected as the imputation of the state.
The tree topologies recovering using Bayesian Inference and Maximum Likelihood were evaluated using the approximately unbiased test [57], implemented in the program CONSEL [58] using the site likelihood scores from PAUP* [59] see Text S1.
For maximum likelihood, the sum of the log likelihoods are evaluated for one-, five- and ten-day returns using overlapping data for the five and ten day returns.
In the recognition phase, the features of an observed object are computed, and class conditional likelihoods are evaluated using Equation 18 for explicit shape model or Equation 19 for implicit shape model.
Likewise, to increase stability of the grid searches, likelihoods were evaluated three times in both the coarse and fine grid searches, and the average of the three evaluations used to determine the range of the finer grid and the selection of models for the final deep sample evaluation.
Finally, since the highest likelihood models can differ only slightly in likelihood values and the evaluating equation [2] can result in slightly different values over multiple runs due to its stochastic nature, the highest likelihood models was evaluated again using M = 1,000,000 samples and the average likelihood over 10 such evaluations was taken.
First, the distribution of likelihood ratios was evaluated empirically by randomly reshuffling the transcript levels of the candidate transcript and recomputing the likelihood ratio (repeating the procedure 100 times).
The significance of the difference in likelihood scores was evaluated using a parametric bootstrap in which 1000 data matrices of 400 bases (the size of the final dataset excluded sites where any individuals had unknown bases) were simulated using the HKY model in Mesquite [75].
The topological stability of the maximum likelihood tree was evaluated by 1000 bootstrap replications.
