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In order to capture the uncertainty around the estimates, 1000 nonparametric bootstrap replications were generated from the sets of multiply imputed data, and mean cost and effect were plotted in a cost effectiveness plane.
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Bootstrapped maximum likelihood trees, 100 replications, were generated with PhyML [ 62] on the PhyML webserver [ 67] using parameters for the substitution model suggested by ModelTest.
Bootstrapped maximum likelihood trees, 100 replications, were generated by PhyML [ 63] on the PhyML webserver [ 70] using parameters for the substitution model suggested by ModelTest.
Five hundred bootstrap replicates were generated.
Neighbor-joining phylogenetic trees (1,000 bootstrap replications) were then generated with SplitsTree4.
Neighbor-joining phylogenetic trees (1,000 bootstrap replications) were then generated by using SplitsTree4 (23 ) and the concatenated sequences of the 7 loci used in the GBS multilocus sequence typing (MLST) scheme.
For each data set, 1000 bootstrap replications were used, resulting in a bootstrap percentile confidence interval for the AMA.
Bootstrap re-sampling was conducted stratified by gastroenterologist; 1,000 bootstrap replications were performed.
The MEGA5 program using the Neighbor-Joining method with default parameters besides 1000 bootstrap replications was used to generate the phylogenetic tree (Tamura et al. 2011), which was further edited by using the Interactive Tree of Life on line tool (iTOL, http://itol.embl.de) (Letunic and Bork 2016).
The Maximum Likelihood method, based on the JTT matrix-based model [ 58] and with 1000 bootstrap replications, was used to generate a phylogenetic tree (Additional file 1: Figure S2).
Clustering and PCA (Principal Component Analysis) are integrated to obtain a more informative feature space, where Feature subspaces and bootstrap replications are implemented orderly to generate more accuracy and diverse base learners.
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