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For all the remaining methods, networks were inferred using the complete dataset (all perturbations simultaneously).
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MRP TNT) was also fast (finishing in under 5 minutes on all these datasets), but the remaining methods were much slower: MRL RAxML) often took more than 1.5 hours and MRP PAUP*) took close to an hour on the 1000-taxon datasets.
The remaining methods all have type I error rates close to or less than the critical values.
Examining the second group of experiments reveals the slightly better performance in terms of precision and recall for methods 3, 4, and 5 (they all exhibit similar performance) compared to the remaining methods (i.e., methods 6, 7, and 8).
Despite the small differences by individual metrics, Figure 5 shows that these five methods exhibit comparable performance: no method outperforms the remaining methods across all metrics and the maximal difference by any metric is within 0.05. Figure 5(a) and 5(b) show two concave curves of Pearson (Truth) and Spearman (Truth) for RNA-Skim by varying its sig-mer length.
On all these model conditions, gMRP had higher accuracy than the remaining methods.
Four of the remaining methods are heuristic.
The remaining methods are not readily available.
The mean RF distances for MinCut, SuperQP and SDM are between 1% and 2% and all remaining methods show an average RF distance of ≤1%.
Figure 1 shows the quadrant analysis: cold turkey, NRT and gradual reduction were in Quadrant I; GP advice was in Quadrant II; prescribed medication and online programs were in Quadrant III; and all remaining methods were in Quadrant IV.
Attach all the remaining petals using the above methods.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com