2022
DOI: 10.1126/sciadv.abj9204
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A better index for analysis of co-occurrence and similarity

Abstract: Scientists often need to know whether pairs of entities tend to occur together or independently. Standard approaches to this issue use co-occurrence indices such as Jaccard, Sørensen-Dice, and Simpson. We show that these indices are sensitive to the prevalences of the entities they describe and that this invalidates their interpretability. We propose an index, α, that is insensitive to prevalences. Published datasets reanalyzed with both α and Jaccard’s index ( J ) yield profoundly diff… Show more

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Cited by 32 publications
(70 citation statements)
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“…Survival was analyzed using the Kaplan-Meier method and Cox regression analysis. The similarity between different HPD definitions and MNL was evaluated by Jaccard index, which was defined as the intersection over union [6,16]. Survival ROC package was used to determine the best cutoff value of new lesions [17].…”
Section: Discussionmentioning
confidence: 99%
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“…Survival was analyzed using the Kaplan-Meier method and Cox regression analysis. The similarity between different HPD definitions and MNL was evaluated by Jaccard index, which was defined as the intersection over union [6,16]. Survival ROC package was used to determine the best cutoff value of new lesions [17].…”
Section: Discussionmentioning
confidence: 99%
“…Since HPD was defined as a rapid increase in tumor burden and was associated with worse clinical outcome [6][7][8], MNL should be taken into account when defining HPD. Jaccard index was defined as the ratio of intersection and union between two sets [16]. It was calculated to evaluate the similarity between MNL and different HPD definitions, as the low Jaccard index value suggested that they included few patients in common.…”
Section: Discussionmentioning
confidence: 99%
“…Sequencing individual ticks also provided sufficient resolution for co-occurrence analyses. We assessed whether presence of one microbial genus increases the statistical likelihood that another microbial genus will be present in the same tick host 46 . This revealed 14 pairs of bacterial genera detected together in a statistically significant number of samples (Figure S3).…”
Section: Optimized Workflow Enables Detection Of Low-abundance Bacter...mentioning
confidence: 99%
“…To determine whether any pairings of taxa (either bacterial or viral) occur more or less frequently than expected given their prevalence we utilized the recently developed metric 𝞪 46 . The presence of each taxon was considered at the genus level for bacteria and at the species level for viruses.…”
Section: Co-occurrence Of Taxamentioning
confidence: 99%
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