R/clopper.pearson.ci.R

In GenBinomApps: Clopper-Pearson Confidence Interval and Generalized Binomial Distribution

clopper.pearson.ci <-
function(k,n,alpha=0.1,CI="upper"){
    l<-round(k)
    if ( is.na(k) || k < 0 || max(abs(k - l)) > 1e-07) 
      stop("'k' must be nonnegative and integer")
    m<-round(n)
    if ( is.na(n) || n < k || max(abs(n - m)) > 1e-07) 
      stop("'n' must be nonnegative and integer >= k")
    if(alpha<0 || alpha>1) {
      stop("'alpha' must be a number between 0 and 1")}
    if(CI=="upper")
    {
      ll<-0
      if(k==n){
        ul=1
      } else{ ul<-qbeta(1-alpha,k+1,n-k)}}
    else if (CI=="lower") 
    {
      ul<-1
      if(k==0){
        ll=0
      }else{ ll<-qbeta(alpha,k,n-k+1)}}
    else if (CI=="two.sided")
    {ll<-qbeta(alpha/2,k,n-k+1)
    ul<-qbeta(1-alpha/2,k+1,n-k)
    if(k==0){
      ll=0
    } else if(k==n){
      ul=1
    }}
    else 
      stop("undefined CI detected")
    data.frame(Confidence.Interval=CI,Lower.limit=ll,Upper.limit=ul,alpha=alpha,row.names="")}