R/IRT.jackknife.gdina.R

In CDM: Cognitive Diagnosis Modeling

## File Name: IRT.jackknife.gdina.R
## File Version: 0.26

###########################################################################
IRT.jackknife.gdina <- function( object, repDesign, ... )
{

    rdes <- repDesign
    # read control arguments
    ctl <- object$control
    # replicate weights
    wgtrep <- repDesign$wgtrep
    RR <- ncol(wgtrep)
    # convert polychoric correlations
    pcvec <- CDM.polychorList2vec(polychorList=object$polychor)
    # assess modelfit
    fmod <- IRT.modelfit( object )$modelfit.stat
    fitvars <- c("MADcor","SRMSR", "100*MADRESIDCOV")
    # read parameter table
    partable <- object$partable

    #**** create parameter table
    jpartable <- partable
    jpartable$skillclass <- jpartable$varyindex <- jpartable$fixed <-
            jpartable$free <- jpartable$totindex <- jpartable$rule <- NULL
    jpartable$group <- NULL
    #---- polychoric correlation
    dfr <- data.frame("partype"="polychor", "parindex"=NA, "item"=0,
                "item.name"="", "parnames"=names(pcvec),
                "value"=pcvec )
    rownames(dfr) <- NULL
    jpartable <- rbind( jpartable, dfr )
    #----- model fit
    dfr <- data.frame("partype"="modelfit", "parindex"=NA, "item"=0,
                "item.name"="", "parnames"=fitvars,
                "value"=fmod[ fitvars, "est" ] )
    rownames(dfr) <- NULL
    jpartable <- rbind( jpartable, dfr )
    #---------------------------------------
    # read control parameters for GDINA function
    args1 <- c( "skillclasses",  "q.matrix", "conv.crit",
                    "dev.crit",  "maxit",   "linkfct", "Mj",
                    "group","method","delta.designmatrix","delta.basispar.lower",
                    "delta.basispar.upper","delta.basispar.init","zeroprob.skillclasses",
                    "reduced.skillspace","HOGDINA","Z.skillspace",
                    "weights","rule", "increment.factor",
                    "fac.oldxsi","avoid.zeroprobs", "delta.fixed"
                        )

    inputlist <- list( "data"=object$data,
                    "delta.init"=object$delta, "attr.prob.init"=ctl$attr.prob )
    A1 <- length(args1)
    for (vv in 1:A1){
        a.vv <- args1[vv]
        inputlist[[ a.vv ]] <- ctl[[ a.vv ]]
    }
    inputlist$progress <- FALSE
    inputlist$calc.se <- FALSE

    #-----------------------------------
    # create jackknife parameter table
    NP <- nrow(jpartable)
    parsM <- matrix( NA, nrow=NP, ncol=RR)
    rownames(parsM) <- jpartable$parnames
    NP1 <- nrow( object$partable )

    #*****************************************
    # loop over datasets
    # cat("0  |" )
    for (rr in 1:RR){
        if ( rr %% 10==1 ){
            cat( paste0( "\n",rr-1, " |" ))
            utils::flush.console()
        }
        inputlist$weights <- rdes$wgtrep[,rr]
        mod1a <- do.call( gdina, inputlist )
        # convert polychoric correlations
        pcvec <- CDM.polychorList2vec(polychorList=mod1a$polychor)
        # assess modelfit
        fmod <- IRT.modelfit( mod1a)$modelfit.stat
        parsM[ 1:NP1, rr ] <- mod1a$partable$value
        parsM[ jpartable$partype=="polychor", rr ] <- pcvec
        parsM[ jpartable$partype=="modelfit", rr ] <- fmod[ fitvars, "est" ]
        cat("-") ; utils::flush.console()
        if ( rr %% 10==0 ){
            cat( paste0( "|" ))
            utils::flush.console()
        }
    }
    cat("\n")
    fayfac <- rdes$fayfac
    res0 <- jkestimates( est=jpartable$value, parsM, fayfac  )
    jpartable$jkest <- res0$dfr$jkest
    jpartable$jkse <- res0$dfr$jkse
    jpartable$t <- jpartable$jkest / jpartable$jkse
    jpartable$p <- 2*stats::pnorm( - abs( jpartable$t ) )

    res <- list( "parsM"=parsM, "vcov"=res0$vcov_pars,
                "jpartable"=jpartable, "fayfac"=fayfac )
    class(res) <- "IRT.jackknife"
    return(res)
}
###########################################################################
summary.IRT.jackknife <- function( object, digits=3,  ... )
{
    obji <- object$jpartable
    V1 <- which( colnames(obji)=="value" )
    V2 <- ncol(obji)
    for (vv in V1:V2){
        obji[,vv] <- round( obji[,vv], digits )
    }
    print(obji)
}
################################################
coef.IRT.jackknife <- function( object,  bias.corr=FALSE, ... )
{
    obji <- object$jpartable
    if ( bias.corr ){
        vari <- "jkest"
    } else {
        vari <- "value"
    }
    vec <- obji[, vari ]
    names(vec) <- obji$parnames
    return(vec)
}
##################################################
vcov.IRT.jackknife <- function( object, ... )
{
    return(object$vcov)
}
##################################################