R: Predict edges based on a hierarchical random graph model

predict_edges {igraph} | R Documentation

## Predict edges based on a hierarchical random graph model

### Description

`predict_edges` uses a hierarchical random graph model to predict missing edges from a network. This is done by sampling hierarchical models around the optimum model, proportionally to their likelihood. The MCMC sampling is stated from `hrg`, if it is given and the `start` argument is set to `TRUE`. Otherwise a HRG is fitted to the graph first.

### Usage

    predict_edges(
      graph,
      hrg = NULL,
      start = FALSE,
      num.samples = 10000,
      num.bins = 25
    )

### Arguments

`graph` | The graph to fit the model to. Edge directions are ignored in directed graphs.
`hrg` | A hierarchical random graph model, in the form of an `igraphHRG` object. `predict_edges`s allow this to be `NULL` as well, then a HRG is fitted to the graph first, from a random starting point.
`start` | Logical, whether to start the fitting/sampling from the supplied `igraphHRG` object, or from a random starting point.
`num.samples` | Number of samples to use for consensus generation or missing edge prediction.
`num.bins` | Number of bins for the edge probabilities. Give a higher number for a more accurate prediction.

### Value

A list with entries:

`edges` | The predicted edges, in a two-column matrix of vertex ids.
`prob` | Probabilities of these edges, according to the fitted model.
`hrg` | The (supplied or fitted) hierarchical random graph model.

### References

A. Clauset, C. Moore, and M.E.J. Newman. Hierarchical structure and the prediction of missing links in networks. Nature 453, 98–101 (2008);

A. Clauset, C. Moore, and M.E.J. Newman. Structural Inference of Hierarchies in Networks. In E. M. Airoldi et al. (Eds.): ICML 2006 Ws, Lecture Notes in Computer Science 4503, 1–13. Springer-Verlag, Berlin Heidelberg (2007).

### See Also

Other hierarchical random graph functions: `consensus_tree()`, `fit_hrg()`, `hrg-methods`, `hrg_tree()`, `hrg()`, `print.igraphHRGConsensus()`, `print.igraphHRG()`, `sample_hrg()`

### Examples

    ## We are not running these examples any more, because they
    ## take a long time (~15 seconds) to run and this is against the CRAN
    ## repository policy. Copy and paste them by hand to your R prompt if
    ## you want to run them.

    ## Not run:
    ## A graph with two dense groups
    g <- sample_gnp(10, p=1/2) + sample_gnp(10, p=1/2)
    hrg <- fit_hrg(g)
    hrg

    ## The consensus tree for it
    consensus_tree(g, hrg=hrg, start=TRUE)

    ## Prediction of missing edges
    g2 <- make_full_graph(4) + (make_full_graph(4) - path(1,2))
    predict_edges(g2)

    ## End(Not run)

[Package igraph version 1.3.1 Index]