R/mice.impute.2l.latentgroupmean.ml.R

In miceadds: Some Additional Multiple Imputation Functions, Especially for 'mice'

## File Name: mice.impute.2l.latentgroupmean.ml.R
## File Version: 2.162

mice.impute.2l.latentgroupmean.ml <- function (y, ry, x, type,
            pls.facs=NULL, imputationWeights=NULL, interactions=NULL, quadratics=NULL,
            EAP=FALSE, ...)
{
    require_namespace("lme4")
    # latent group mean
    cluster <- as.numeric( x[, type==- 2] )
    covariates <- as.matrix( x[, type==1 ] )
    colnames(covariates) <- colnames(x)[ type==1 ]
    y <- x[, type==2 ]
    # distinguish cases with and without covariates
    if ( sum( type==1 ) > 0){
        cov2 <- cbind( cluster, covariates )
        # aggregate covariates
        covaggr <- mice.impute.2l.groupmean( y, ry, x=cov2,
                        type=c(-2, rep(1, ncol(covariates) ) ),
                        grmeanwarning=FALSE )
        colnames(covaggr) <- colnames(covariates)
        # aggregation at level 2
        covaggr.l2 <- stats::aggregate( covaggr, list( cluster ), mean )
        colnames(covaggr.l2)[-1] <- colnames(covaggr)
        y.l2 <- stats::aggregate( y, list( cluster ), mean, na.rm=TRUE )
        h1 <- as.matrix(covaggr.l2[,-1] )
        colnames(h1) <- colnames(covaggr)
        # PLS interactions and quadratics
        res <- mice_imputation_get_states(pos=parent.frame(n=1) )
        vname <- res$vname
        newstate <- res$newstate
        plsout <- mice_imputation_pls_helper( newstate=newstate, vname=vname,
                        pls.impMethod="xplsfacs", x=h1, y=y.l2[,2],
                        ry=( ! is.na(y.l2[,2] )),
                        imputationWeights=rep( 1, nrow(covaggr.l2)),
                        interactions=interactions, quadratics=quadratics,
                        pls.facs=pls.facs, ... )
        # imputation PLS
        if( ! is.null( plsout$yimp  ) ){
            covaggr.l2r <- as.matrix(plsout$yimp[,-1])
            covaggr <- as.matrix( covaggr.l2r[ match(cluster,covaggr.l2[,1]),])
        }
        mod <- lme4::lmer( y ~ as.matrix(covaggr) + ( 1 | cluster ) )
    } else {
        mod <- lme4::lmer( y ~ ( 1 | cluster ) )
    }
    modr <- lme4::ranef( mod, condVar=TRUE )
    modr <- modr$cluster
    modf <- mod@resp$mu
    # extract cluster indices
    a1 <- stats::aggregate( modf, list( cluster), mean )
    a1[,3] <-  sqrt( attr( modr, "postVar" )[1,1,] )
    # match cluster indices
    ind <- match( cluster, a1[,1] )
    ximp <- stats::rnorm( nrow(a1), mean=a1[,2],  sd=(1-EAP)*a1[,3] )[ ind ]
    return(ximp)
}


mice.impute.2l.latentgroupmean.ML <- mice.impute.2l.latentgroupmean.ml