version 1.0-5

ChangeLog

@@ -1,3 +1,8 @@
+2015-08-20  1.0-5  - So called Vos-Hudson adjustment implemented.
+                   - DESCRIPTION corrected.
+                   - Imports from stats added to NAMESPACE.
+                   - Documentation edited.
+
 2014-05-07  1.0-4  Algorithms improved:
                    - An incorrect (and, fortunately, almost never used) branch
                      removed from binom.blaker.lower.limit.R.

DESCRIPTION

@@ -1,16 +1,14 @@
 Package: BlakerCI
 Type: Package
-Title: Blaker's binomial confidence limits
-Version: 1.0-4
-Date: 2014-05-07
+Title: Blaker's Binomial Confidence Limits
+Version: 1.0-5
+Date: 2015-08-20
 Author: Jan Klaschka
 Maintainer: Jan Klaschka <klaschka@cs.cas.cz>
-Description: Fast and accurate calculation of 
-	Blaker's binomial confidence limits
-	(and some related stuff)
-License: GPL-2
+Description: Fast and accurate calculation of Blaker's binomial confidence limits (and some related stuff).
+License: GPL-3
 LazyLoad: yes
-Packaged: 2014-05-06 19:54:43 UTC; klaschka
 NeedsCompilation: no
+Packaged: 2015-08-20 15:45:10 UTC; klaschka
 Repository: CRAN
-Date/Publication: 2014-05-07 23:35:18
+Date/Publication: 2015-08-20 19:52:46

MD5

@@ -1,11 +1,16 @@
-eeeb878922147817fc8fd6028f2cf6f9 *ChangeLog
-a73e4e800296623ff377abfd0438bcba *DESCRIPTION
-76b309ced09fde087399bf426fe6bbaa *NAMESPACE
+9677a0469d8f43c4c0bda58d24473b77 *ChangeLog
+aeff792d2d47edf07c21f9f1f67a3a86 *DESCRIPTION
+622d97f1a2f90799930a4cd04c5a3258 *NAMESPACE
+8f41fbda3173ebf87f028f2479cbd70b *R/binom.blaker.VHadj.acc.R
+7bd74de7a2337bd2e96a08a9ba3f7c94 *R/binom.blaker.VHadj.limits.R
+b81d0a0e4af032ee3c7a781fcce33e29 *R/binom.blaker.VHadj.lower.limit.R
 38f9b537d00dba55ae6a2717721bdbdd *R/binom.blaker.acc.R
 e31a8b5ad8ee890e82fa31bc5777b9f4 *R/binom.blaker.acc.single.p.R
 cfa0c40d1cbd95045c3400212df7a4d6 *R/binom.blaker.limits.R
 83a0de528aa33eb2acae2965b561638b *R/binom.blaker.lower.limit.R
-afd954c6de1e31cad77d458048675f81 *man/BlakerCI-internal.Rd
-f9d6fb28066f558da9f6a32c779c3e29 *man/BlakerCI-package.Rd
-ed48c280ca2556fcbb9e607e263c0985 *man/binom.blaker.acc.Rd
-db02a5c5631ff08520055cf56e1dfd95 *man/binom.blaker.limits.Rd
+f65871c4eefefd0a087c3baed147f43d *man/BlakerCI-internal.Rd
+dc046f448f61ede62eb7e81f31ac9965 *man/BlakerCI-package.Rd
+c7739d5ea97fd342138aa25528d5dc4f *man/binom.blaker.VHadj.acc.Rd
+158ec2cc80c7eccf4fb4209e7726b8a2 *man/binom.blaker.VHadj.limits.Rd
+f1a7c77709703911bc5b6306381576d0 *man/binom.blaker.acc.Rd
+0b2164dd6cd538fc2278ca83bb9ce32f *man/binom.blaker.limits.Rd

NAMESPACE

@@ -1 +1,3 @@
-export(binom.blaker.lower.limit,binom.blaker.limits,binom.blaker.acc.single.p,binom.blaker.acc)
+importFrom("stats", "pbinom", "qbinom", "qbeta", "pbeta")
+export(binom.blaker.lower.limit,binom.blaker.limits,binom.blaker.acc.single.p,binom.blaker.acc,
+       binom.blaker.VHadj.lower.limit,binom.blaker.VHadj.limits,binom.blaker.VHadj.acc)

R/binom.blaker.VHadj.acc.R

@@ -0,0 +1,42 @@
+binom.blaker.VHadj.acc <- function(x,n,p,type=c("orig","unimod"),acc.tol=1e-10,nmax=n+1000,int.eps=1e-12,...) {
+  if (n < 1 || x < 0 || x > n) stop("Parameters n = ",n,", x = ",x, " wrong!")
+  if (acc.tol <= 0) stop("Numerical tolerance ",acc.tol," nonpositive!")
+  type <- match.arg(type)
+  if (type != "orig" && type != "unimod") stop("Unknown type ",type,"!")
+  m <- length(p)
+  if (m < 1) stop("Empty vector p!")
+  acc <- binom.blaker.acc(x,n,p,type=type,acc.tol=acc.tol,...=...)
+  nn <- n+1
+  ind.susp <- 1:length(p)
+  ind.susp1 <- ind.susp[p[ind.susp] <= x/n]
+  ind.susp2 <- ind.susp[p[ind.susp] >  x/n]
+  repeat {
+    if (nn > nmax) {
+      warning("n = ", n, ", x = ", x,": Upper limit of ", nmax, 
+              " too low, Vos-Hudson adjustment may be incomplete.") 
+      break
+    }
+    xx <- x*nn/n
+    aa1 <- pmin(2*pbeta(p[ind.susp1],xx,nn-xx+1),1)
+    aa2 <- pmin(2*pbeta(1-p[ind.susp2],nn-xx,xx+1),1)
+    ind.susp1 <- ind.susp1[aa1 > acc[ind.susp1]]    
+    ind.susp2 <- ind.susp2[aa2 > acc[ind.susp2]]    
+    if (length(ind.susp1) + length(ind.susp2) < 1) break
+    acc.nn.L <- numeric(0)
+    acc.nn.R <- numeric(0)
+    if (length(ind.susp1) > 0) {
+      x.star <- ceiling(xx-int.eps)
+      acc.nn.L <- binom.blaker.acc(x.star,nn,p[ind.susp1],type=type,acc.tol=acc.tol,...=...)
+    }
+    if (length(ind.susp2) > 0) {
+      x.star <- floor(xx+int.eps)
+      acc.nn.R <- binom.blaker.acc(x.star,nn,p[ind.susp2],type=type,acc.tol=acc.tol,...=...)
+    }
+    acc.nn <- c(acc.nn.L,acc.nn.R)
+    ind.susp <- c(ind.susp1,ind.susp2)
+    acc[ind.susp] <- pmax(acc[ind.susp],acc.nn)
+    nn <- nn+1
+  }
+
+  acc
+}

R/binom.blaker.VHadj.limits.R

@@ -0,0 +1,8 @@
+binom.blaker.VHadj.limits <- function(x,n,level=.95,tol=1e-10,...) {
+  if (n < 1 || x < 0 || x > n) stop("Parameters n = ",n,", x = ",x, " wrong!")
+  if (level <= 0 || level >= 1) stop("Confidence level ",level," out of (0, 1)!")
+  if (tol <= 0) stop("Numerical tolerance ",tol," nonpositive!")
+  lower <- binom.blaker.VHadj.lower.limit(x,n,level,tol,...)
+  upper <- 1 - binom.blaker.VHadj.lower.limit(n-x,n,level,tol,...)
+  return(c(lower,upper))
+}

R/binom.blaker.VHadj.lower.limit.R

@@ -0,0 +1,23 @@
+binom.blaker.VHadj.lower.limit <- function(x,n,level,tol=1e-10,maxiter=100,nmax=n+1000,int.eps=1e-10) {
+  if (x <=0) return(0)
+  if (x>0) {
+    lower <- binom.blaker.lower.limit(x,n,level,tol,maxiter)
+    alpha <- 1-level
+    nn <- n
+    p <- x/n
+    repeat {
+      nn <- nn+1
+      xstar <- nn*p
+      if (qbeta(alpha/2,xstar,nn-xstar+1) > lower) break
+      if (nn > nmax) {
+         warning("n = ", n, ", x = ", x,": Upper limit of ", nmax, 
+                 " too low, Vos-Hudson adjustment may be incomplete.") 
+         break
+      }
+      xx <- ceiling(xstar-int.eps)
+      ll <- binom.blaker.lower.limit(xx,nn,level,tol,maxiter)
+      lower <- min(lower,ll)
+    }
+  }
+  return(lower)
+}

man/BlakerCI-internal.Rd

@@ -2,18 +2,22 @@
 \alias{BlakerCI-internal}
 \alias{binom.blaker.lower.limit}
 \alias{binom.blaker.acc.single.p}
+\alias{binom.blaker.VHadj.lower.limit}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
 Internal functions, not expected to be called by the user.
 }
 \description{
-Calculation of the lower Blaker's confidence limit 
-(\code{binom.blaker.lower.limit}) 
-and a single acceptability value -- unmodified or \sQuote{unimodalized}
+Calculation of the lower Blaker's confidence limit
+as defined by Blaker (\code{binom.blaker.lower.limit}),
+or with so called Vos-Hudson adjustment (\code{binom.blaker.VHadj.lower.limit});
+a single acceptability value, optionally \dQuote{unimodalized}
 (\code{binom.blaker.acc.single.p}).
 }
 \usage{
 binom.blaker.lower.limit(x, n, level, tol = 1e-10, maxiter=100)
+binom.blaker.VHadj.lower.limit(x,n,level,tol=1e-10,maxiter=100,
+      nmax=n+1000,int.eps=1e-10)
 binom.blaker.acc.single.p(x, n, p, type = "orig", acc.tol = 1e-10,
       output = "acc", maxiter=100)
 }
@@ -35,7 +39,8 @@ binom.blaker.acc.single.p(x, n, p, type = "orig", acc.tol = 1e-10,
       point (single value between 0 and 1) where to calculate the acceptability.
 }
   \item{type}{
-      "orig", or "unimod" -- either unmodified, or unimodalized acceptability \cr
+      \code{"orig"}, or \code{"unimod"} -- either unmodified, or unimodalized 
+      acceptability \cr
       (see \code{\link{binom.blaker.acc}}).      
 }
   \item{acc.tol}{
@@ -52,19 +57,35 @@ binom.blaker.acc.single.p(x, n, p, type = "orig", acc.tol = 1e-10,
       Maximum number of interval halving iterations during the search
       for a confidence limit (\code{binom.blaker.lower.limit}) or
       a discontinuity point of the acceptability function 
-      (\code{binom.blaker.acc.single.p} with \code{type} \code{=} \code{"unimod"}). 
+      (\code{binom.blaker.acc.single.p} with \code{type = "unimod"}). 
       When the required accuracy is not reached in \code{maxiter} steps -- 
       typically when too small \code{tol} or \code{acc.tol}
       exceeds capabilities of machine arithmetic -- last step's result
       is returned with warning.
 }
 
+  \item{nmax}{
+      Pairs \code{(y, m)} of number of trials and number of successes 
+      are allowed to contribute to the Vos-Hudson adjustment for only
+      \code{m} up to \code{nmax}. Warning is returned when greater
+      numbers of trials are suspect to have influence.
+}
+  \item{int.eps}{
+      Maximum expected error of machine representation of integers
+      calculated via multiplication and division from reals.
+      (Used in order to round numbers correctly if they happen
+      to be integer, e. g.
+      \code{ceiling(xx - int.eps)} is calculated instead of 
+      \code{ceiling(xx)}.)
+}
+
 }
 %\details{
 %%  ~~ If necessary, more details than the description above ~~
 %}
 \value{
-For \code{binom.blaker.lower.limit}, a single number -- 
+For \code{binom.blaker.lower.limit} and
+\code{binom.blaker.VHadj.lower.limit}, a single number -- 
 the lower confidence limit. \cr
 For \code{binom.blaker.acc.single.p} -- depending on the
 \code{output} parameter -- a single acceptability value, or a single
@@ -83,7 +104,8 @@ Jan Klaschka \email{klaschka@cs.cas.cz}
 %% ~Make other sections like Warning with \section{Warning }{....} ~
 
 \seealso{
-\code{\link{binom.blaker.limits}}, \code{\link{binom.blaker.acc}}.
+\code{\link{binom.blaker.limits}}, \code{\link{binom.blaker.VHadj.limits}},\cr
+\code{\link{binom.blaker.acc}}, \code{\link{binom.blaker.VHadj.acc}}.
 }
 %\examples{
 %}

man/BlakerCI-package.Rd

@@ -13,9 +13,9 @@ confidence limits.
 \tabular{ll}{
 Package: \tab BlakerCI\cr
 Type: \tab Package\cr
-Version: \tab 1.0-4\cr
-Date: \tab 2014-05-07\cr
-License: \tab GPL-2\cr
+Version: \tab 1.0-5\cr
+Date: \tab 2015-08-20\cr
+License: \tab GPL-3\cr
 LazyLoad: \tab yes\cr
 }
 }
@@ -55,7 +55,7 @@ Maintainer: Jan Klaschka \email{klaschka@cs.cas.cz}
 \section{Acknowledgement}{
 This work was accomplished with institutional support RVO:67985807. 
 
-Previous versions were supported by grant 205/09/1079 from 
+Versions up to 1.0-2 were supported by grant 205/09/1079 from 
 The Czech Science Foundation.
 %
 %I am grateful to Petr Savicky for a valuable e-mail