Mostly wrapper functions that can be used in conjunction with indirect_relations to fine tune indirect relations.

dist_2pow(x) dist_inv(x) dist_dpow(x, alpha = 1) dist_powd(x, alpha = 0.5) walks_limit_prop(x) walks_exp(x, alpha = 1) walks_exp_even(x, alpha = 1) walks_exp_odd(x, alpha = 1) walks_attenuated(x, alpha = 1/max(x) * 0.99) walks_uptok(x, alpha = 1, k = 3)

x | Matrix of relations. |
---|---|

alpha | Potential weighting factor. |

k | For walk counts up to a certain length. |

Transformed relations as matrix

The predefined functions follow the naming scheme `relation_transformation`

.
Predefined functions `walks_*`

are thus best used with type="walks" in
indirect_relations. Theoretically, however, any transformation can be used with any relation.
The results might, however, not be interpretable.

The following functions are implemented so far:
`dist_2pow`

returns \(2^{-x}\)
`dist_inv`

returns \(1/x\)
`dist_dpow`

returns \(x^{-\alpha}\) where \(\alpha\) should be chosen greater than 0.
`dist_powd`

returns \(\alpha^x\) where \(\alpha\) should be chosen between 0 and 1.
`walks_limit_prop`

returns the limit proportion of walks between pairs of nodes. Calculating
rowSums of this relation will result in the principle eigenvector of the network.
`walks_exp`

returns \(\sum_{k=0}^\infty \frac{A^k}{k!}\)
`walks_exp_even`

returns \(\sum_{k=0}^\infty \frac{A^{2k}}{(2k)!}\)
`walks_exp_odd`

returns \(\sum_{k=0}^\infty \frac{A^{2k+1}}{(2k+1)!}\)
`walks_attenuated`

returns \(\sum_{k=0}^\infty \alpha^k A^k\)
`walks_uptok`

returns \(\sum_{j=0}^k \alpha^j A^j\)

Walk based transformation are defined on the eigen decomposition of the adjacency matrix using the fact that $$f(A)=Xf(\Lambda)X^T.$$ Care has to be taken when using user defined functions.