Bayesian network learning with compositional data {Compositional}R Documentation

Bayesian network learning with compositional data

Description

Bayesian network learning with compositional data.

Usage

compbn(x, type = "fedhc", max_k = 3, alpha = 0.05, robust = FALSE,
ini.stat = NULL, R = NULL, restart = 10, tabu = 10, score = "bic-g",
blacklist = NULL, whitelist = NULL)

Arguments

x

A numerical matrix with the compositional data. They can be either the logged compositional or the centred log-ratio transformed compositional data. We leave this open to the user.

type

This can be either "fedhc", "pchc", "mmhc", "fedtabu", "pctabu" or "mmtabu".

max_k

The maximum conditioning set to use in the conditional indepedence test (see Details). Integer, default value is 3

alpha

The significance level for assessing the p-values.

robust

Do you want outliers to be removed prior to applying the algorithms? If yes, set this to TRUE to utilise the MCD.

ini.stat

If the initial test statistics (univariate associations) are available, pass them through this parameter.

R

If the correlation matrix is available, pass it here.

restart

An integer, the number of random restarts.

tabu

An integer, the length of the tabu list used in the tabu function.

score

A character string, the label of the network score to be used in the algorithm. If none is specified, the default score is the Bayesian Information Criterion. Other available scores are: "bic-g" (default), "loglik-g", "aic-g", "bic-g" or "bge".

blacklist

A data frame with two columns (optionally labeled "from" and "to"), containing a set of arcs not to be included in the graph.

whitelist

A data frame with two columns (optionally labeled "from" and "to"), containing a set of arcs to be included in the graph.

Details

The FEDHC algorithm is implemented. The FBED algortihm (Borboudakis and Tsamardinos, 2019), without the backward phase, is implemented during the skeleton identification phase. Next, the Hill Climbing greedy search or the Tabu search is employed to score the network.

The PC algorithm as proposed by Spirtes et al. (2001) is first implemented followed by a scoring phase, such as hill climbing or tabu search. The PCHC was proposed by Tsagris (2021), while the PCTABU algorithm is the same but instead of the hill climbing scoring phase, the tabu search is employed.

The MMHC algorithm is implemented without performing the backward elimination during the skeleton identification phase. The MMHC as described in Tsamardinos et al. (2006) employs the MMPC algorithm during the skeleton construction phase and the Tabu search in the scoring phase. In this package, the mmhc function employs the Hill Climbing greedy search in the scoring phase while the mmtabu employs the Tabu search.

Value

A list including:

ini

A list including the output of the mmhc.skel function.

dag

A "bn" class output. A list including the outcome of the Hill-Climbing or the Tabu search phase. See the package "bnlearn" for more details.

scoring

The score value.

runtime

The duration of the algorithm.

Author(s)

Michail Tsagris.

R implementation and documentation: Michail Tsagris mtsagris@uoc.gr.

References

Tsagris M. (2021). A new scalable Bayesian network learning algorithm with applications to economics. Computational Economics, 57(1):341-367.

Tsagris M. (2021). The FEDHC Bayesian network learning algorithm. https://arxiv.org/pdf/2012.00113.pdf.

Borboudakis G. and Tsamardinos I. (2019). Forward-backward selection with early dropping. Journal of Machine Learning Research, 20(8): 1-39.

Tsamardinos I., Brown E.L. and Aliferis F.C. (2006). The max-min hill-climbing Bayesian network structure learning algorithm. Machine Learning, 65(1): 31-78.

Spirtes P., Glymour C. and Scheines R. (2001). Causation, Prediction, and Search. The MIT Press, Cambridge, MA, USA, 3nd edition.

See Also

acor, alr, alfa

Examples

# simulate a dataset with continuous data
x <- rdiri( 100, runif(20) )
a <- compbn( log(x) )

[Package Compositional version 5.2 Index]