############################これ以降をRGuiに貼り付けてください########################
cohen.kappa1<-
function (classif, type = c("score", "count")) 
{
    if (missing(classif)) 
        stop("Usage: cohen.kappa(classif, type=\"score\")\n")
    if (!is.numeric(classif)) 
        classif <- apply(apply(classif, 2, as.factor), 2, as.numeric)
    if (type[1] == "score") 
        classif.mat <- scores.to.counts(classif)
    else classif.mat <- as.matrix(classif)
    minclassif <- min(classif.mat)
    classdim <- dim(classif)
    k <- apply(classif.mat, 1, sum)
    if (any(k != k[1])) {
        classif.mat <- cbind(classif.mat, max(k) - k)
        k <- apply(classif.mat, 1, sum)
        cat("Different row sums, a no-classification category was added.\n\n")
    }
    matdim <- dim(classif.mat)
    N <- matdim[1]
    ncat <- matdim[2]
    if (type[1] == "score") {
        if (any(is.na(classif))) {
            cat("Can't use Cohen's method with NAs\n")
            PEc <- NA
        }
        else {
            pj <- apply(apply(classif, 2, tabulate, nbins = ncat)/N, 
                1, prod)
            PEc <- sum(pj)
        }
    }
    else PEc <- NA
    Cj <- apply(classif.mat, 2, sum)
    pj <- Cj/(N * k[1])
    PEsc <- sum(pj^2)
    Si <- 1/(k[1] * (k[1] - 1)) * sum(classif.mat * (classif.mat - 
        1))
    PA <- (1/N) * sum(Si)
    Ksc <- (PA - PEsc)/(1 - PEsc)
    if (type[1] == "score") {
        Kc <- (PA - PEc)/(1 - PEc)
        varKc <- (2/(N * k[1] * (k[1] - 1))) * (PEc - (2 * k[1] - 
            3) * PEc^2 + 2 * (k[1] - 2) * sum(pj^3))/(1 - PEc)^2
        Zc <- Kc/sqrt(varKc)
        pc <- 1 - pnorm(Zc)
    }
    else {
        Kc <- NA
        Zc <- NA
        pc <- NA
    }
    varKsc <- (2/(N * k[1] * (k[1] - 1))) * (PEsc - (2 * k[1] - 
        3) * PEsc^2 + 2 * (k[1] - 2) * sum(pj^3))/(1 - PEsc)^2
    Zsc <- Ksc/sqrt(varKsc)
    psc <- 1 - pnorm(Zsc)
    Kbbc <- 2 * PA - 1
Q0<-1-PA
Qe<-1-PEc
Qe.sc<-1-PEsc
sigma.k<-sqrt((PA*Q0)/(N*Qe^2))
Kc.upper<-Kc+qnorm(0.975)*sigma.k
Kc.lower<-Kc-qnorm(0.975)*sigma.k
sigma.ksc<-sqrt((PA*Q0)/(N*Qe.sc^2))
Ksc.upper<-Ksc+qnorm(0.975)*sigma.ksc
Ksc.lower<-Ksc-qnorm(0.975)*sigma.ksc
    k<-c(kappa.c = Kc, Zc = Zc,pc = pc,Kc.lower=Kc.lower,Kc.upper=Kc.upper,kappa.sc = Ksc, Zsc = Zsc, kappa.bbc = psc,Ksc.lower=Ksc.lower,Ksc.upper=Ksc.upper)
   kr<-t(matrix(k,5,2))
dimnames(kr)<-list(c("Kappa(Cohen)","Kappa(Siegel)"),c("coef.","Z","p","95%CI-lower","95%CI-upper"))
kr
}
scores.to.counts<-
function (scores) 
{
    if (is.data.frame(scores)) 
        score.names <- levels(as.factor(as.vector(unlist(scores))))
    if (is.matrix(scores)) 
        score.names <- levels(as.factor(as.vector(scores)))
    if (missing(score.names)) 
        stop("scores must be a data frame or matrix")
    score.levels <- as.numeric(score.names)
    nlevels <- length(score.levels)
    nobj <- length(scores[, 1])
    counts <- matrix(0, nrow = nobj, ncol = nlevels)
    colnames(counts) <- score.names
    for (i in 1:nobj) {
        for (j in 1:nlevels) counts[i, j] <- sum(scores[i, ] == 
            score.levels[j], na.rm = TRUE)
    }
    return(counts)
}

cohen.kappa.r<-
function(x,xcol=2)# xcolはソートしたい列番号．デフォルトで2列目
{
X<-NULL
for(i in 1:nrow(x))
{
x1<-x[-c(i),]
X<-rbind(X,c(i,cohen.kappa1(x1)[1,],cohen.kappa1(x1)[2,]))
}
dimnames(X)[[2]]<-c("No.(omit)","Cohen coef.","Cohen Z","Cohen p","Cohen 95%CI-lower","Cohen 95%CI-upper","Siegel coef.","Siegel Z","Siegel p","Siegel 95%CI-lower","Siegel 95%CI-upper")
list("各行番号の行を除いた係数が降順にソートされて出力される（行名が「5」のときは5行目のデータ以外で計算）"=X[order(X[,xcol],decreasing=T),]
)
}