fastmode: Rapidly converging algorithm for calculating posterior modes...

Description Usage Arguments Details Value References See Also Examples

View source: R/lmm.R


Computes the marginal posterior mode of the variance parameters in linear mixed models using a rapidly converging procedure described by Schafer (1998), which combines Fisher scoring with an ECME algorithm. The method is a minor modification of the restricted maximum-likelihood (RML) procedure used in "fastrml". The model is identical to that of "fastrml" with the addition of prior distributions for the variance parameters.

For a description of the prior distribution, see the "Details" section below.


fastmode(y, subj, pred, xcol, zcol, prior, vmax, occ, start,
   maxits=100, eps=0.0001)


Identical to those for the function "fastrml", with one additional required argument:


vector of responses. This is simply the individual yi vectors stacked upon one another. Each element of y represents the observed response for a particular subject-occasion, or for a particular unit within a cluster.


vector of same length as y, giving the subject (or cluster) indicators i for the elements of y. For example, suppose that y is c(y1,y2,y3,y4) where length(y1)=2, length(y2)=3, length(y3)=2, and length(y4)=7. Then subj should be c(1,1,2,2,2,3,3,4,4,4,4,4,4,4).


matrix of covariates used to predict y. The number of rows should be length(y). The first column will typically be constant (one), and the remaining columns correspond to other variables appearing in Xi and Zi.


vector of integers indicating which columns of pred will be used in Xi. That is, pred[,xcol] is the Xi matrices (stacked upon one another.


vector of integers indicating which columns of pred will be used in Zi. That is, pred[,zcol] is the Zi matrices (stacked upon one another).


A list with four components specifying the hyperparameters of the prior distribution applied to sigma2 and psi. The components must be named "a", "b", "c", and "Dinv". All are scalars except for "Dinv", which is a matrix of dimension c(length(zcol),length(zcol)).


optional matrix of dimension c(max(occ),max(occ)) from which the Vi matrices will be extracted. In a longitudinal dataset, vmax would represent the Vi matrix for an individual with responses at all possible occasions 1,2,...,nmax=max(occ); for individuals with responses at only a subset of these occasions, the Vi will be obtained by extracting the rows and columns of vmax for those occasions. If no vmax is specified by the user, an identity matrix is used. In most applications of this model one will want to have Vi = identity, so most of the time this argument can be omitted.


vector of same length as y indicating the "occasions" for the elements of y. This argument is relevant only if a non-identity vmax is specified. In a longitudinal dataset where each individual is measured on at most nmax distinct occasions, each element of y corresponds to one subject-occasion, and the elements of occ should be coded as 1,2,...,nmax to indicate these occasion labels. (You should label the occasions as 1,2,...,nmax even if they are not equally spaced in time; the actual times of measurement will be incorporated into the matrix "pred".)


optional starting values of the parameters. If this argument is not given then the function chooses its own starting values. This argument should be a list of three elements named "beta", "psi", and "sigma2". Note that "beta" should be a vector of the same length as "xcol", "psi" should be a matrix of dimension c(length(zcol),length(zcol)), and "sigma2" should be a scalar.


maximum number of cycles to be performed. The algorithm runs to convergence or until "maxits" iterations, whichever comes first.


convergence criterion. The algorithm is considered to have converged if the relative differences in all parameters from one iteration to the next are less than eps–that is, if all(abs(new-old)<eps*abs(old)).


The algorithm is described in the appendix of Schafer (1998). Scoring is carried out on log(sigma2) and the nonredundant elements of the inverse of psi/sigma2, taking logs of the diagonal elements. Upon convergence, the estimates represent the mode of the joint posterior density of 1/sigma2 and the inverse of psi, marginalized (i.e. integrated) over beta.

The prior distribution applied to the within-unit residual variance is scaled inverted-chisquare,

sigma2 ~ a / chisq(b),

where chisq(b) denotes a chisquare random variable with b degrees of freedom, and a and b are user-defined hyperparameters. Values for the hyperparmeters may be chosen by regarding a/b as a rough prior guess for sigma2, and as the imaginary degrees of freedom on which this guess is based.

The prior distribution applied to the between-unit covariance matrix is inverted Wishart,

psiinv ~ W(c,D),

where psiinv is the inverse of the between-unit covariance matrix psi, and W(c,D) denotes a Wishart distribution with degrees of freedom c and scale matrix D. Values for the hyperparameters may be chosen by regarding Dinv/c (the inverse of D divided by c) as a rough prior guess for psi, and c as the imaginary degrees of freedom on which this guess is based.

An improper uniform prior density function is applied to the fixed effects beta.


a list containing the following components.


vector of same length as "xcol" containing estimated fixed effects. This estimate represents the posterior mean for beta, conditional upon the estimated values of the variance parameters sigma2 and psi.


estimate of residual error variance.


matrix of dimension c(length(zcol),length(zcol)) containing estimated variances and covariances of the random effects.


T if the algorithm converged, F if it did not.


number of iterations actually performed. Will be equal to "maxits" if converged=F.


a logical vector of length iter indicating, for each iteration, whether the scoring estimates were rejected and replaced by ECME estimates (T), or whether the scoring estimates were accepted (F). Scoring estimates are rejected if they do not increase the log-posterior density.


vector of length "iter" reporting the value of the log-posterior density at each iteration.


matrix of dimension c(length(xcol),length(xcol)) containing estimated variances and covariances for elements of "beta". These are conventional estimates which regard the variance parameters (sigma2 and psi) as fixed at their estimated values.


Schafer, J.L. (1998) Some improved procedures for linear mixed models. Submitted to Journal of the American Statistical Association.

See Also

ecmeml, ecmerml, fastml, fastrml, mgibbs, fastmcmc, example


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For a detailed example, see the file "example.R" distributed
with this library.

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lmm documentation built on July 8, 2020, 6:28 p.m.