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Of the measures recommended in here the authors used four, namely accuracy, specificity, sensitivity, and MCC and the remaining row wise parameters could be calculated from the confusion tables.
In the column wise parameters, which are for the ratios of either positive or negative cases (sensitivity and specificity), are not affected whereas there is a significant difference in NPV and PPV, which are row wise ratios based on numbers of both positive and negative cases.
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All sequences were aligned using Geneious default values, with pair-wise parameters set at gap opening penalty 10, gap extension penalty 0.1 and multiple alignment parameters set at gap opening penalty of 10, gap extension 0.2.
The unrestricted 'partial credit' Rasch polytomous model was used with conditional pair-wise parameter estimation [ 16].
The unrestricted (partial credit) Rasch polytomous model was used with a conditional pair-wise parameter estimation [ 30].
The likelihood is minimized using an iterative optimization algorithm involving step-wise parameter adjustments and repeated simulations.
In step 4b, we use the k-means clustering algorithm to divide the sites in the focal subset into two clusters based on one or more of the site-wise parameter estimates from step 4a.
Voxel-wise parameter estimates for these regressors were obtained by restricted maximum-likelihood estimation, using a temporal high-pass filter (cut-off 128 s) to remove low-frequency drifts, and modeling temporal autocorrelation across scans with an AR(1) process.
These terms are then normalized by the total variance to obtain first and second-order sensitivity indices corresponding to the main effect of each parameter, and the effects from pair-wise parameter interactions [ 14]. (See Additional file 1 for mathematical formulas).
Voxel-wise parameter estimates for these regressors were obtained by restricted maximum-likelihood estimation (ReML), using a temporal high-pass filter (cut-off 128 secs) to remove low-frequency drifts, and modelling temporal autocorrelation across scans with an Auto-regression (1) process.
Voxel-wise parameter estimates for these covariates were obtained by restricted maximum-likelihood (ReML) estimation, using a temporal high-pass filter (cut-off 128 s) to remove low-frequency drifts, and modeling temporal autocorrelation across scans with an AR(1) process.
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