mixture.model: Mixture model

Description Usage Arguments Value Author(s) References Examples

Description

Fit Gaussian mixture model

Usage

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mixture.model(
  x,
  mixture.method = "vdp",
  max.responses = 10,
  implicit.noise = 0,
  prior.alpha = 1,
  prior.alphaKsi = 0.01,
  prior.betaKsi = 0.01,
  vdp.threshold = 1e-05,
  initial.responses = 1,
  ite = Inf,
  speedup = TRUE,
  bic.threshold = 0,
  pca.basis = FALSE,
  min.responses = 1,
  ...
)

Arguments

x

data matrix (samples x features, for multivariate analysis) or a vector (for univariate analysis)

mixture.method

Specify the approach to use in mixture modeling. Options. vdp (nonparametric Variational Dirichlet process mixture model); bic (based on Gaussian mixture modeling with EM, using BIC to select the optimal number of components)

max.responses

Maximum number of responses for each subnetwork. Can be used to limit the potential number of network states.

implicit.noise

Implicit noise parameter. Add implicit noise to vdp mixture model. Can help to avoid overfitting to local optima, if this appears to be a problem.

prior.alpha, prior.alphaKsi, prior.betaKsi

Prior parameters for Gaussian mixture model that is calculated for each subnetwork (normal-inverse-Gamma prior). alpha tunes the mean; alphaKsi and betaKsi are the shape and scale parameters of the inverse Gamma function, respectively.

vdp.threshold

Minimal free energy improvement after which the variational Gaussian mixture algorithm is deemed converged.

initial.responses

Initial number of components for each subnetwork model. Used to initialize calculations.

ite

Maximum number of iterations on posterior update (updatePosterior). Increasing this can potentially lead to more accurate results, but computation may take longer.

speedup

Takes advantage of approximations to PCA, mutual information etc in various places to speed up calculations. Particularly useful with large and densely connected networks and/or large sample size.

bic.threshold

BIC threshold which needs to be exceeded before a new mode is added to the mixture with mixture.method = "bic"

pca.basis

pca.basis

min.responses

minimum number of responses

...

Further optional arguments to be passed.

Value

List with two elements: model: fitted mixture model (parameters and free energy); model.params: model parameters

Author(s)

Contact: Leo Lahti leo.lahti@iki.fi

References

See citation("netresponse")

Examples

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netresponse documentation built on Nov. 8, 2020, 5:04 p.m.