Accuracy of ClassTR’s classification on 9 simulated datasets conditional on correct resolution.

<p>Accuracy of ClassTR’s classification on 9 simulated datasets conditional on correct resolution.</p

Example of the ClassTR classification.

<p><b>Top right</b> The precursor sets (in the unweighted constant metric) indicated by arrows from the simple strains chosen to cover the third complex strain <b>Bottom</b> Its final classification given by ClassTR</p

Example of the ClassTR resolution.

<p><b>a</b>. A dataset containing 3 simple strains (<i>F</i> in the problem description) and 3 complex strains (<i>C</i> in the problem description) <b>b</b>. The 2 possible resolutions of the third complex strain (<i>q</i> = 2) into simple strains (the first complex strain has 1 possible resolution (<i>q</i> = 1) and the second one, 4 possible resolutions (<i>q</i> = 3)); the resolution chosen by ClassTR is framed <b>c</b>. The three initial (<i>F</i> in the problem description) and two newly added (<i>S</i> in the problem description) simple strains that form the unique optimal solution, with arrows indicating the resolution of complex strains into simple strains</p

Percent accuracy of classification methods on simulated datasets.

<p>Percent accuracy of classification methods on simulated datasets.</p

Percent accuracy of ClassTR’s classification on 9 simulated datasets; mutation rates: low, 0.00012; medium, 0.0012; high, 0.012; reinfection rates: low, 0.012; medium, 0.04; high, 0.12 (per year); the percentage in brackets is the corresponding accuracy for the standard method.

<p>Percent accuracy of ClassTR’s classification on 9 simulated datasets; mutation rates: low, 0.00012; medium, 0.0012; high, 0.012; reinfection rates: low, 0.012; medium, 0.04; high, 0.12 (per year); the percentage in brackets is the corresponding accuracy for the standard method.</p

Percent accuracy of ClassTR’s strain resolution on 9 simulated datasets; mutation rates: low, 0.00012; medium, 0.0012; high, 0.012; reinfection rates: low, 0.012; medium, 0.04; high, 0.12 (per year); the percentage in brackets is the corresponding accuracy for the method of picking a random resolution.

<p>Percent accuracy of ClassTR’s strain resolution on 9 simulated datasets; mutation rates: low, 0.00012; medium, 0.0012; high, 0.012; reinfection rates: low, 0.012; medium, 0.04; high, 0.12 (per year); the percentage in brackets is the corresponding accuracy for the method of picking a random resolution.</p

Classification results of the standard method and ClassTR on the South African dataset.

<p>Classification results of the standard method and ClassTR on the South African dataset.</p

Bivariate and multivariate association with culture positive TB at time of death.

<p>Bivariate and multivariate association with culture positive TB at time of death.</p

Study population characteristics.

<p>Study population characteristics.</p

Postmortem smear and culture status among participants, categorized by TB treatment status.

<p>Postmortem smear and culture status among participants, categorized by TB treatment status.</p