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All 10 markers including c Kit remained highly significant for prognostic prediction of metastasis (P-value of deviance increase=0.0411).
The ranking of c Kit was 2 out of 25, based on odd ratios and P-values of deviance increase (Table 3).
As the counts of lipofuscin granules (Fig 5D) are expressed as discrete numbers, these were analyzed by deviance from a Negative Binomial generalized linear models (Venables & Ripley, 2002) (P value analysis of deviance: Fig 5D: 1.7 × 10 7).
When grouping all cohorts into a unique cohort group, the model with the significantly lowest value of residual deviance included length and age and their interaction.
One simply computes as the average of D θ| y) over the posterior samples of θ, and as the value of the deviance at the average of the posterior samples of θ.
An overfit model will always have a higher value of adjusted deviance than a simpler model nested within it, but its predictive power to an independent sample will be lower because the model losses generality.
Goodness-of-fit of the final models were evaluated visually by comparing the estimated cumulative probability distributions from the negative binomial model to the observed cumulative probability distribution and comparing the value of the deviance factor statistic and the Pearson's chi-squared statistic to 1.
n ^ : Estimate of the number of diagnoses not reported to any source; N ^ : Estimate of the number of diagnoses; 95% CI: 95% confidence interval for N ^ ; df: number of degrees of freedom; G: deviance statistic; p: p-value of the deviance goodness-of-fit test; AIC: Akaike Information Criterion DICC: Draper Information Criterion.
Values of the deviance residual >2.5 were considered outliers and were excluded from the final analysis.
Analyses of 500 combinations of tree complexity (ranging from 3 to 7) and learning rate (ranging from 0.001 to 0.01) produced models with between 450 and 3900 trees whose values of predictive deviance ranged from 0.582 to 0.624.
While the strictly additive trend test EGT appears to be marginally preferable compared with the proportional odds trend test GTE, there is little information with which to choose between the 2 tests at low values of dominance deviance.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com