R/mcdina.R

In CDM: Cognitive Diagnosis Modeling

## File Name: mcdina.R
## File Version: 0.936


#- Multiple Choice DINA Model
#- mcdina model (de la Torre, 2009)
mcdina <- function( dat, q.matrix, group=NULL,
            itempars="gr", weights=NULL, skillclasses=NULL,
            zeroprob.skillclasses=NULL,  reduced.skillspace=TRUE,
            conv.crit=0.0001, dev.crit=.1, maxit=1000, progress=TRUE )
{
    # prepare data
    s1 <- Sys.time()
    cl <- match.call()
    dat <- as.matrix(dat)

    # zero/one entries, q.matrix from ordinary DINA model
    res0 <- mcdina_proc_qmatrix( dat=dat, q.matrix=q.matrix )
    dat <- res0$dat
    q.matrix0 <- q.matrix <- res0$q.matrix

    # handle polytomous attributes
    res1 <- mcdina_proc_modify_qmatrix( q.matrix=q.matrix, skillclasses=skillclasses )
    q.matrix <- res1$q.matrix
    q.matrix0 <- res1$q.matrix0
    skillclasses <- res1$skillclasses
    skillclasses0 <- res1$skillclasses0
    maxmaxattr <- res1$maxmaxattr

    #- data check
    res <- mcdina_check_data(dat=dat, q.matrix=q.matrix)

    dat0 <- dat
    dat_na <- is.na(dat)
    dat.resp <- 1* ( 1 - dat_na )
    dat_resp_bool <- ! dat_na
    dat[ dat.resp==0 ] <- 1
    dat_ <- dat - 1
    eps <- 1e-10
    I <- ncol(dat)    # number of items
    CC <- max( q.matrix[,2] )  # maximal number of categories
    K <- ncol(q.matrix)-2  # number of skills
    if (K<=3 ){ reduced.skillspace <- FALSE }
    # group identifier
    if ( is.null(group) ){ group <- rep(1,nrow(dat))}
    group0 <- group
    group0_unique <- sort( unique( group ) )
    group <- match( group, group0_unique )
    group <- group - 1
    G <- length( unique(group) )
    # weights
    if ( is.null(weights) ){ weights <- rep(1,nrow(dat))}

    # define skill classes
    if ( is.null(skillclasses) ){
        skillclasses <- as.matrix( expand.grid(
                as.data.frame( rbind( rep(0,K), rep(1,K)  ) ) ) )
    }
    classes <- cdm_matrixstring( matr=skillclasses, string="P" )
    rownames(skillclasses) <- classes
    TP <- nrow(skillclasses)
    # define specification of estimation of item parameters
    if ( mean( itempars=="gr" )==1 ){
        itempars <- rep( "gr", I )
    }
    if ( ( mean( itempars=="gr" ) < 1 ) & ( length(itempars) !=I ) ){
        itempars <- rep( "jo", I )
    }

    # prepare latent responses
    res <- mcdina_proc_test_latent_response( q.matrix=q.matrix, K=K, TP=TP,
                skillclasses=skillclasses, classes=classes )
    lc <- res$lc
    lr <- res$lr
    itemstat <- res$itemstat
    itemstat$G <- G
    itemstat$partype <- itempars
    itemstat$N.pars <- itemstat$N.lr * (itemstat$N.cat - 1 )
    itemstat$N.pars <- ifelse( itemstat$partype=="gr",
            itemstat$N.pars*itemstat$G, itemstat$N.pars )
    # list of lr
    lc_list <- lr_list <- list(1:I)
    for (ii in 1:I){
        lr_list[[ii]] <- lr[ lr$item==ii, ]
        lc_list[[ii]] <- lc[ lc$item==ii, ]
    }

    # delta parameter inits
    res <- mcdina_init_delta( lc=lc, lr=lr )
    delta_ideal <- res$delta_ideal
    delta0 <- res$delta

    # delta parameters
    delta <- array( 0,  dim=c(I,CC,CC,G) )
    for (gg in 1:G){
        delta[,,,gg] <- delta0
    }
    # init probabilities
    probs <- array( 0, dim=c(I,CC,TP,G ) )

    # init latent class distribution
    pi.k <- rep( 1 / TP, TP )
    pi.k <- matrix( pi.k, nrow=TP, ncol=G )

    # counts latent responses
    lr_counts <- array(0, dim=c(I,CC,G) )

    #*****************************
    # define reduced skillspace
    Z <- Z.skillspace <- NULL
    if ( reduced.skillspace ){
        A <- skillclasses
        attr.patt <- skillclasses
        maxAttr <- 1
        # combinations
        kombis <- utils::combn( K, 2 )
        KK <- ncol(kombis)
        B <- NULL
        for (kk in 1:KK){
            B <- cbind( B, attr.patt[, kombis[1,kk] ] * attr.patt[, kombis[2,kk] ] )
        }
        Z <- cbind( 1, A, B )
        ncolZ <- ncol(Z)
        v1 <- c("Int",  paste("A",1:K, sep="") )
        v1 <- c(v1,apply( kombis, 2, FUN=function(ll){
            paste( paste( "A", ll, sep=""), collapse="_" ) } ))
        colnames(Z) <- v1

        m1 <- which( maxAttr > 1 )
        if ( max(maxAttr) > 1 ){
            Z1 <- Z[, m1, drop=FALSE ]^2
            colnames(Z1) <- paste0( colnames(q.matrix)[m1], "*2")
            Z <- cbind( Z, Z1 )
        }
        if ( ! is.null(Z.skillspace) ){
            Z <- Z.skillspace
        }
        # check for equal columns
        Z <- Z[, ! duplicated( t(Z) ) ]
        ncolZ <- ncol(Z)
    }

    iter <- dev <- 0
    max.par.change <- 1000
    devchange <- 100
    # display for progress
    disp <- "...........................................................\n"

    #****************************************
    #************ begin algorithm ***********
    while ( ( iter < maxit ) &
                ( ( max.par.change > conv.crit ) | ( devchange > dev.crit  ) )
                    )
    {

    #z0 <- Sys.time()
        #--- (0) collect old parameters
        dev0 <- dev
        delta0 <- delta

        #--- (1) calculate probabilities
        for (gg in 1:G){ # gg <- 1
            for (ii in 1:I){    # ii <- 1
                lr.ii <- lr_list[[ii]]
                probs[ii,,,gg] <- delta[ ii,, lr.ii$lr_index, gg]
            }
        }
# cat("calc probs ") ; z1 <- Sys.time(); print(z1-z0) ; z0 <- z1

        #--- (2) calculate likelihood
        probs_ <- as.matrix( array( probs, dim=c(I, CC*TP*G) ) )
        res <- cdm_rcpp_mcdina_probs_pcm_groups( dat=dat_, dat_resp_bool=dat_resp_bool,
                        group=group, probs=probs_, CC=CC, TP=TP )
        f.yi.qk <- res$fyiqk
# cat("calc like ") ; z1 <- Sys.time(); print(z1-z0) ; z0 <- z1

        #--- (3) calculate posterior and expected counts
        res1 <- cdm_rcpp_mcdina_calccounts_pcm_groups( dat=dat_, dat_resp_bool=dat_resp_bool,
                        group=group, fyiqk=f.yi.qk, pik=pi.k, CC=CC, weights=weights )
        n.ik <- array( res1$nik, dim=c( I, CC, TP, G ) )
        count_pik <- res1$count_pik
        for (gg in 1:G){
            pi.k[,gg] <- count_pik[,gg] / sum( count_pik[,gg] )
        }
        # set some probabilities of skill classes to zero
        if ( ! is.null(zeroprob.skillclasses ) ){
            pi.k[ zeroprob.skillclasses, ] <- 0
        }
        LL <- res1$LL
        dev <- -2*LL
        f.qk.yi <- res1$fqkyi
# cat("calc post ") ; z1 <- Sys.time(); print(z1-z0) ; z0 <- z1

        #--- (4) log-linear smoothing of skill class distribution
        if (reduced.skillspace){
            pi.k <- mcdina_est_reduced_skillspace(pi.k=pi.k, Z=Z)
        }
# cat("calc smoothing distribution") ; z1 <- Sys.time(); print(z1-z0) ; z0 <- z1

        #--- (5) calculate updated item parameters
        res1 <- mcdina_est_item( n.ik=n.ik, lr_list=lr_list, lc_list=lc_list,
                    delta=delta, I=I, G=G, eps=eps, itemstat=itemstat,
                    itempars=itempars, lr_counts=lr_counts )
        delta <- res1$delta
        lr_counts <- res1$lr_counts
# cat("calc item parameters") ; z1 <- Sys.time(); print(z1-z0) ; z0 <- z1

        #--- (11) convergence
        max.par.change <- max( abs( delta - delta0 ) )
        devchange <- abs( dev- dev0)
        iter <- iter + 1

        #--- (99) display progress
        if (progress) {
            cat(disp)
            cat("Iteration", iter, "   ", paste( Sys.time() ), "\n" )
            cat( "Deviance=", round( dev, 5 ) )
            g11 <-  - ( dev - dev0 )
            if (iter >1){
                cat(" | Deviance change=", round( -(dev-dev0), 7) )
                if (g11 < 0 ){
                    cat( "\n**** Deviances decreases! Check for nonconvergence.   ****\n")
                }
            }
            cat("\n" )
            cat("Maximum parameter change:", round( max.par.change, 6), "\n")
            utils::flush.console()
        }
    }
    #*************** end algorithm ***********
    #*****************************************

    # include information criteria
    ic <- mcdina_calc_ic( dev=dev, weights=weights, itemstat=itemstat, pi.k=pi.k,
                G=G, I=I, zeroprob.skillclasses=zeroprob.skillclasses,
                reduced.skillspace=reduced.skillspace, Z=Z )

    # include standard error
    se.delta <- mcdina_calc_se_delta( delta=delta, n.ik=n.ik, probs=probs,
                    lr_list=lr_list, lc_list=lc_list, itemstat=itemstat, I=I, G=G,
                    itempars=itempars, lr_counts=lr_counts, CC=CC )

    # labeling
    rownames(pi.k) <- classes
    colnames(pi.k) <- paste0("Group.", group0_unique )

    # rename skill classes in case of polytomous attributes
    if (maxmaxattr > 1 ){
        skillclasses <- skillclasses0
        lc$Q <- cdm_matrixstring(q.matrix0[,-c(1:2) ], "Q" )
        q.matrix <- q.matrix0
    }

    # item summary table
    item <- mcdina_collect_itempars( I=I, lc=lc, itempars=itempars,
                itemstat=itemstat, dat=dat, G=G, CC=CC, delta=delta, se.delta=se.delta,
                group0_unique=group0_unique )

    # skill pattern
    skill.patt <- mcdina_skill_patt( q.matrix=q.matrix, skillclasses=skillclasses,
                            G=G, pi.k=pi.k, group0_unique=group0_unique )

    # person classification
    mle.class <- skillclasses[ max.col( f.yi.qk ), ]
    map.class <- skillclasses[ max.col( f.qk.yi ), ]
    N11 <- nrow(mle.class)
    K11 <-  ncol(mle.class)
    K12 <- nrow(skillclasses)

    eap.class <- matrix( 0, nrow=N11, ncol=K11 )
    colnames(eap.class) <- colnames(mle.class)
    for (kk in 1:K11){
        sckk <- matrix( skillclasses[,kk], nrow=N11, ncol=K12, byrow=TRUE )
        eap.class[,kk] <- rowSums( sckk * f.qk.yi )
    }
    #---- OUTPUT
    res <- list( item=item, posterior=f.qk.yi, like=f.yi.qk, ic=ic,
                q.matrix=q.matrix, pik=probs, delta=delta, se.delta=se.delta,
                itemstat=itemstat, n.ik=n.ik, deviance=dev, attribute.patt=pi.k,
                attribute.patt.splitted=skillclasses, skill.patt=skill.patt,
                MLE.class=mle.class, MAP.class=map.class, EAP.class=eap.class, dat=dat0,
                skillclasses=skillclasses, group=group0, lc=lc, lr=lr, iter=iter,
                itempars=itempars, weights=weights, I=nrow(dat), G=G, CC=CC, loglike=-dev/2,
                AIC=ic$AIC, BIC=ic$BIC, Npars=ic$np )
    res$converged <- iter < maxit
    res$control$weights <- weights
    res$control$group <- group

    s2 <- Sys.time()
    res$time <- list( s1=s1, s2=s2, timediff=s2-s1)
    cat("----------------------------------- \n")
    cat("Start:", paste( s1), "\n")
    cat("End:", paste(s2), "\n")
    cat("Difference:", print(s2 -s1), "\n")
    cat("----------------------------------- \n")
    class(res) <- "mcdina"
    res$call <- cl
    return(res)
}