R: Logarithm of the Marginal Likelihood

LML {LaplacesDemon} | R Documentation

## Logarithm of the Marginal Likelihood

### Description

This function approximates the logarithm of the marginal likelihood (LML), where the marginal likelihood is also called the integrated likelihood or the prior predictive distribution of y in Bayesian inference. The marginal likelihood is

p(y) = integral p(y | Theta)p(Theta) d Theta

The prior predictive distribution indicates what y should look like, given the model, before y has been observed. The presence of the marginal likelihood of y normalizes the joint posterior distribution, p(Theta|y), ensuring it is a proper distribution and integrates to one (see `is.proper`). The marginal likelihood is the denominator of Bayes' theorem, and is often omitted, serving as a constant of proportionality. Several methods of approximation are available.

### Usage

    LML(Model=NULL, Data=NULL, Modes=NULL, theta=NULL, LL=NULL, Covar=NULL,
    method="NSIS")

### Arguments

`Model` | This is the model specification for the model that was updated either in `IterativeQuadrature`, `LaplaceApproximation`, `LaplacesDemon`, `LaplacesDemon.hpc`, or `VariationalBayes`. This argument is used only with the `LME` method.
`Data` | This is the list of data passed to the model specification. This argument is used only with the `LME` method.
`Modes` | This is a vector of the posterior modes (or medians, in the case of MCMC). This argument is used only with the `GD` or `LME` methods.
`theta` | This is a matrix of posterior samples (parameters only), and is specified only with the `GD`, `HME`, or `NSIS` methods.
`LL` | This is a vector of MCMC samples of the log-likelihood, and is specified only with the `GD`, codeHME, or `NSIS` methods.
`Covar` | This argument accepts the covariance matrix of the posterior modes, and is used only with the `GD` or `LME` methods.
`method` | The method may be `"GD"`, `"HME"`, `"LME"`, or `"NSIS"`, and defaults to `"NSIS"`. `"GD"` uses the Gelfand-Dey estimator, `"HME"` uses the Harmonic Mean Estimator, `"LME"` uses the Laplace-Metropolis Estimator, and `"NSIS"` uses nonparametric self-normalized importance sampling (NSIS).

### Details

Generally, a user of `LaplaceApproximation`, `LaplacesDemon`, `LaplacesDemon.hpc`, `PMC`, or `VariationalBayes` does not need to use the `LML` function, because these methods already include it. However, `LML` may be called by the user, should the user desire to estimate the logarithm of the marginal likelihood with a different method, or with non-stationary chains. The `LaplacesDemon` and `LaplacesDemon.hpc` functions only call `LML` when all parameters are stationary, and only with non-adaptive algorithms.

The `GD` method, where GD stands for Gelfand-Dey (1994), is a modification of the harmonic mean estimator (HME) that results in a more stable estimator of the logarithm of the marginal likelihood. This method is unbiased, simulation-consistent, and usually satisfies the Gaussian central limit theorem.

The `HME` method, where HME stands for harmonic mean estimator, of Newton-Raftery (1994) is the easiest, and therefore fastest, estimation of the logarithm of the marginal likelihood. However, it is an unreliable estimator and should be avoided, because small likelihood values can overly influence the estimator, variance is often infinite, and the Gaussian central limit theorem is usually not satisfied. It is included here for completeness. There is not a function in this package that uses this method by default. Given N samples, the estimator is 1 / [1/N sum_N exp(-LL)].

The `LME` method uses the Laplace-Metropolis Estimator (LME), in which the estimation of the Hessian matrix is approximated numerically. It is the slowest method here, though it returns an estimate in more cases than the other methods. The supplied `Model` specification must be executed a number of times equal to k^2 x 2, where k is the number of parameters. In large dimensions, this is very slow. The Laplace-Metropolis Estimator is inappropriate with hierarchical models. The `IterativeQuadrature`, `LaplaceApproximation`, and `VariationalBayes` functions use `LME` when it has converged and `sir=FALSE`, in which case it uses the posterior means or modes, and is itself Laplace Approximation.

The Laplace-Metropolis Estimator (LME) is the logarithmic form of equation 4 in Lewis and Raftery (1997). In a non-hierarchical model, the marginal likelihood may easily be approximated with the Laplace-Metropolis Estimator for model m as

p(y|m) = (2*pi)^(d_m/2) |Sigma_m|^(1/2) p(y|Theta_m, m)p(Theta_m|m)

where d is the number of parameters and Sigma is the inverse of the negative of the approximated Hessian matrix of second derivatives.

As a rough estimate of Kass and Raftery (1995), LME is worrisome when the sample size of the data is less than five times the number of parameters, and LME should be adequate in most problems when the sample size of the data exceeds twenty times the number of parameters (p. 778).

The `NSIS` method is essentially the `MarginalLikelihood` function in the `MargLikArrogance` package. After `HME`, this is the fastest method available here. The `IterativeQuadrature`, `LaplaceApproximation`, and `VariationalBayes` functions use `NSIS` when converged and `sir=TRUE`. The `LaplacesDemon`, `LaplacesDemon.hpc`, and `PMC` functions use `NSIS`. At least 301 stationary samples are required, and the number of parameters cannot exceed half the number of stationary samples.

### Value

`LML` returns a list with two components:

`LML` | This is an approximation of the logarithm of the marginal likelihood (LML), which is notoriously difficult to estimate. For this reason, several methods are provided. The marginal likelihood is useful when comparing models, such as with Bayes factors in the `BayesFactor` function. When the method fails, `NA` is returned, and it is most likely that the joint posterior is improper (see `is.proper`).
`VarCov` | This is a variance-covariance matrix, and is the negative inverse of the Hessian matrix, if estimated. The `GD`, `HME`, and `NSIS` methods do not estimate `VarCov`, and return `NA`.

### Author(s)

Statisticat, LLC. software@bayesian-inference.com

### References

Gelfand, A.E. and Dey, D.K. (1994). "Bayesian Model Choice: Asymptotics and Exact Calculations". Journal of the Royal Statistical Society, Series B 56, p. 501–514.

Kass, R.E. and Raftery, A.E. (1995). "Bayes Factors". Journal of the American Statistical Association, 90(430), p. 773–795.

Lewis, S.M. and Raftery, A.E. (1997). "Estimating Bayes Factors via Posterior Simulation with the Laplace-Metropolis Estimator". Journal of the American Statistical Association, 92, p. 648–655.

Newton, M.A. and Raftery, A.E. (1994). "Approximate Bayesian Inference by the Weighted Likelihood Bootstrap". Journal of the Royal Statistical Society, Series B 3, p. 3–48.

### See Also

`BayesFactor`, `is.proper`, `IterativeQuadrature`, `LaplaceApproximation`, `LaplacesDemon`, `LaplacesDemon.hpc`, `PMC`, and `VariationalBayes`.

### Examples

    ### If a model object were created and called Fit, then:
    #
    ### Applying HME to an object of class demonoid or pmc:
    #LML(LL=Fit$Deviance*(-1/2), method="HME")
    #
    ### Applying LME to an object of class demonoid:
    #LML(Model, MyData, Modes=apply(Fit$Posterior1, 2, median), method="LME")
    #
    ### Applying NSIS to an object of class demonoid
    #LML(theta=Fit$Posterior1, LL=Fit$Deviance*-(1/2), method="NSIS")
    #
    ### Applying LME to an object of class iterquad:
    #LML(Model, MyData, Modes=Fit$Summary1[,1], method="LME")
    #
    ### Applying LME to an object of class laplace:
    #LML(Model, MyData, Modes=Fit$Summary1[,1], method="LME")
    #
    ### Applying LME to an object of class vb:
    #LML(Model, MyData, Modes=Fit$Summary1[,1], method="LME")

[Package LaplacesDemon version 16.1.1 Index]