R/mi.anova.R

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

## File Name: mi.anova.R
## File Version: 0.366


mi.anova <- function( mi.res, formula, type=2 )
{
    mi.list <- mi.res
    if( inherits(mi.list,"mids.1chain") ){
        mi.list <- mi.list$midsobj
    }
    if( inherits(mi.list,"mids") ){
        # number of imputations
        m <- mi.list$m
        # list of completed datasets
        h1 <- list( rep("", m ))
        for (ii in 1:m){
            h1[[ii]] <- as.data.frame( mice::complete( mi.list, ii ) )
        }
        mi.list <- h1
    }
    # converting mi.norm objects
    if (inherits(mi.res,"mi.norm") ){
        mi.list <- mi.list$imp.data
    }
    #**** type II sum of squares
    if (type==2){
        anova.imp0 <- lapply( mi.list, FUN=function(dat){
                        stats::lm( formula, data=dat ) } )
        anova.imp <- lapply( anova.imp0, FUN=function(obj){
                    summary( stats::aov(obj))
                            } )
    }
    #**** type III sum of squares
    if (type==3){
        require_namespace("car")
        Nimp <- length(mi.list)
        vars <- all.vars( stats::as.formula( formula ))[-1]
        VV <- length(vars)
        # define contrasts
        ma_contrasts <- as.list(1:VV)
        names(ma_contrasts) <- vars
        dat <- mi.list[[1]]
        for (vv in 1:VV){
            ma_contrasts[[ vars[vv] ]] <- "contr.sum"
            if ( ! is.factor( dat[, vars[vv] ]  ) ){
                    ma_contrasts[[ vars[vv] ]] <- NULL
            }
        }
        # estimate linear model
        anova.imp0 <- lapply( as.list( 1:Nimp), FUN=function(ii){
            dat <- mi.list[[ii]]
            mod1 <- stats::lm( formula, data=dat, contrasts=ma_contrasts)
            return(mod1)
        } )
        # compute summary
        anova.imp <- lapply( as.list( 1:Nimp), FUN=function( ii ){
                obj <- anova.imp0[[ii]]
                car::Anova(obj, type=3)
                    }
                )
    }

    # number of F statistics to be evaluated
    if (type==2){
        FF <- nrow( anova.imp[[1]][[1]] ) - 1
    }
    if (type==3){
        FF <- nrow(anova.imp[[1]]["F value"])-2
    }
    anova.imp.inf <- t( sapply( 1:FF, FUN=function(ff){
            micombine.F( sapply( 1:( length(anova.imp) ), FUN=function(ii){
                        if ( type==2 ){
                          r1 <- anova.imp[[ii]][[1]]$'F value'[ff]
                        }
                        if ( type==3 ){
                          r1 <- anova.imp[[ii]]$'F value'[ff+1]
                        }
                        return(r1)
                                    } ),
                            df1=ifelse (type==2, anova.imp[[1]][[1]]$Df[ff],
                                         anova.imp[[1]]["Df"][ff+1,1] ),
                            display=FALSE )
                } ) )

    # ANOVA results
    res <- anova.imp.inf[, c(3,4,1,2) ]
    res <- matrix( res, ncol=4 )
    res[,3] <- round( res[,3], 4 )
    res[,4] <- round( res[,4], 6 )
    g1 <- rownames( anova.imp[[1]][[1]] )[1:FF]
    if (type==3){ g1 <-    rownames( anova.imp[[1]] )[1 + 1:FF] }
    rownames(res) <- g1
    res <- data.frame(res)

    # compute eta squared and partial eta squared coefficients
    if (type==2){
        SS <- rowMeans( matrix( unlist( lapply( anova.imp, FUN=function(ll){
                ll[[1]][,2] } ) ), ncol=length(mi.list) )  )
    }
    if (type==3){
        SS <- rowMeans( matrix( unlist( lapply( anova.imp, FUN=function(ll){
                l2 <- ll["Sum Sq"][-1,1]
                return(l2)
                        } ) ), ncol=length(mi.list) )  )
    }

    # calculate (average) R squared
    r.squared <-  sum(SS[ - (FF+1) ]) / sum(SS)
    res$eta2 <- round( SS[ - ( FF + 1 ) ] / sum( SS ), 6 )
    res$partial.eta2 <- round( SS[ - (FF+1) ] / ( SS[ - (FF+1) ] + SS[ FF + 1 ] ), 6 )
    g1 <- c("F value", "Pr(>F)" )
    colnames(res)[3:4] <- g1
    colnames(res)[1:2] <- c("df1", "df2")
    c1 <- colnames(res)
    res <- rbind( res, res[1,] )
    rownames( res)[ nrow(res) ]  <- "Residual"
    res[ nrow(res), ] <- NA
    res <- data.frame( "SSQ"=SS, res )
    colnames(res)[-1] <- c1
    cat("Univariate ANOVA for Multiply Imputed Data",
                paste0("(Type ", type, ")" ), " \n\n")
    cat("lm Formula: ", formula  )
    cat( paste( "\nR^2=", round(r.squared, 4 ), sep=""), "\n" )
    cat("..........................................................................\n")
    cat("ANOVA Table \n" )
    print( round( res,5) )
    res1 <- list( "r.squared"=r.squared, "anova.table"=res, type=type )
    invisible(res1)
}