mcmc.defaultParams_nonLinear {GRENITS} | R Documentation

## Default Parameters for non-Linear Model

### Description

Create parameter vector with default parameters for NonLinearNet function

### Usage

    mcmc.defaultParams_nonLinear()

### Details

Use this function to generate a template parameter vector to use non-default parameters for the NonLinearNet 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) trunc` | Truncation parameter for InvertedPareto prior on tau (smoothness parameter)
`(7) tau0` | Precision parameter for N(0, tau0^(-0.5)) prior on B (first two coefficients)
`(8) M` | Numer of knots used for each spline function
`(9) a` | Shape parameter for Gamma(a,b) prior on lambda (Regression precision)
`(10) b` | Rate parameter for Gamma(a,b) prior on lambda (Regression precision)
`(11) sigma.mu` | Standard deviation parameter for N(0,sigma.mu) prior on mu (Regression intercept)
`(12) a_pareto` | Pareto parameter for InvertedPareto prior on tau (smoothness parameter)

### References

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`, `NonLinearNet`.

### Examples

        # Get default parameters
        nonLinearNet.params <- mcmc.defaultParams_nonLinear()

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

        # Change prior on smoothness parameter
        nonLinearNet.params[6] <- 30000 # Change truncation
        nonLinearNet.params[12] <- 3 # Concentrate more mass close to linear region

        # Plot to check changes
        plotPriors(nonLinearNet.params)

        ## Use to run LinearNet ...

[Package GRENITS version 1.38.0 Index]