mcmc.defaultParams_Linear {GRENITS} | R Documentation

## Default Parameters for Linear Model

### Description

Create parameter vector with default parameters for LinearNet function

### Usage

    mcmc.defaultParams_Linear()

### Details

Use this function to generate a template parameter vector to use non-default parameters for the LinearNet model.

### Value

Returns a single vector with the following elements (in this order):

`(1) samples` | Number of MCMC iterations to run.
`(2) burn.in` | Number of initial iterations to discard as burn in.
`(3) thin` | Subsampling frequency
`(4) c` | Shape parameter 1 for Beta(c,d) prior on rho (connectivity parameter)
`(5) d` | Shape parameter 2 for Beta(c,d) prior on rho (connectivity parameter)
`(6) sigma.s` | Standard deviation parameter for N(0,sigma.s) prior on B (Regression coefficients)
`(7) a` | Shape parameter for Gamma(a,b) prior on lambda (Regression precision)
`(8) b` | Rate parameter for Gamma(a,b) prior on lambda (Regression precision)
`(9) sigma.mu` | Standard deviation parameter for N(0,sigma.mu) prior on mu (Regression intercept)

### References

Morrissey, E.R., Juarez, M.A., Denby, K.J. and Burroughs, N.J. 2010. On reverse engineering of gene interaction networks using time course data with repeated measurements. Bioinformatics 2010; doi: 10.1093/bioinformatics/btq421

Morrissey, E.R., Juarez, M.A., Denby, K.J. and Burroughs, N.J. 2011 Inferring the time-invariant topology of a nonlinear sparse gene regulatory network using fully Bayesian spline autoregression Biostatistics 2011; doi: 10.1093/biostatistics/kxr009

### See Also

`plotPriors`, `LinearNet`.

### Examples

        # Get default parameters
        linearNet.params <- mcmc.defaultParams_Linear()

        # Change run length
        linearNet.params[1] <- 150000

        # Change prior regression precision
        linearNet.params[7] <- 0.001
        linearNet.params[8] <- 0.001

        # Plot to check changes
        plotPriors(linearNet.params)

        ## Use to run LinearNet ...

[Package GRENITS version 1.34.0 Index]