mixture.model {netresponse} | R Documentation |
Fit Gaussian mixture model
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, ...)
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. |
List with two elements: model: fitted mixture model (parameters and free energy); model.params: model parameters
Contact: Leo Lahti leo.lahti@iki.fi
See citation("netresponse")