co_heaviness | R Documentation |

Co-heaviness for pairs of parent packages

co_heaviness(x, rel = FALSE, a = 10, jaccard = FALSE)

`x` |
An object returned by |

`rel` |
Whether to return the absolute measure or the relative measure. |

`a` |
A constant added for calculating the relative measure. |

`jaccard` |
Whether to return Jaccard coeffcient? |

Denote a package as P and its two strong parent packages as A and B, i.e., parent packages in "Depends", "Imports" and "LinkingTo", the co-heaviness for A and B is calculated as follows.

Denote S_A as the set of reduced dependency packages when only moving A to "Suggests" of P, and denote S_B as the set of reduced dependency
packages when only moving B to "Suggests" of P, denote S_AB as the set of reduced dependency packages when moving A and B together to "Suggests" of P,
the co-heaviness of A, B on P is calculatd as `length(setdiff(S_AB, union(S_A, S_B)))`

, which is the number of reduced package only caused by co-action of A and B.

Note the co-heaviness is only calculated for parent packages in "Depends", "Imports" and "LinkingTo".

When `jaccard`

is set to `TRUE`

, the function returns jaccard coeffcient. `setdiff(S_AB, union(S_A, S_B))`

is actually
the set of dependencies imported by and only by two parent packages A and B. Thus the jaccard coeffcient is calculated as
`length(setdiff(S_AB, union(S_A, S_B)))/length(S_AB)`

.

## Not run: x = pkgndep("DESeq2") hm = co_heaviness(x) ComplexHeatmap::Heatmap(hm) co_heaviness(x, jaccard = TRUE) ## End(Not run)

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