| Title: | Blaker's Binomial and Poisson Confidence Limits |
|---|---|
| Description: | Fast and accurate calculation of Blaker's binomial and Poisson confidence limits (and some related stuff). |
| Authors: | Jan Klaschka |
| Maintainer: | Jan Klaschka <[email protected]> |
| License: | GPL-3 |
| Version: | 1.0-6 |
| Built: | 2024-11-26 06:43:34 UTC |
| Source: | CRAN |
Fast and accurate calculation of Blaker's binomial and Poisson confidence limits.
| Package: | BlakerCI |
| Type: | Package |
| Version: | 1.0-6 |
| Date: | 2019-04-29 |
| License: | GPL-3 |
| LazyLoad: | yes |
This work was accomplished with institutional support RVO:67985807. The same was true for the previous version 1.0-5.
Versions up to 1.0-2 were supported by grant 205/09/1079 from The Czech Science Foundation.
Jan Klaschka [email protected]
Maintainer: Jan Klaschka [email protected]
binom.blaker.limits(3,10) # [1] 0.08726443 0.61941066 poisson.blaker.limits(3) # [1] 0.8176914 8.5597971binom.blaker.limits(3,10) # [1] 0.08726443 0.61941066 poisson.blaker.limits(3) # [1] 0.8176914 8.5597971
Calculates values of the acceptability function for the binomial
distribution (see function acceptbin in Blaker (2000))
in a sequence of points (for, e.g., plotting purposes).
The acceptability function may optionally be
“unimodalized”, i.e. replaced with the smallest
greater or equal unimodal function.
binom.blaker.acc(x, n, p, type = c("orig", "unimod"), acc.tol = 1e-10, ...)binom.blaker.acc(x, n, p, type = c("orig", "unimod"), acc.tol = 1e-10, ...)
x |
number of successes. |
n |
number of trials. |
p |
vector (length 1 allowed) of hypothesized binomial parameters (between 0 and 1). In case of more than one point, an increasing sequence required. |
type |
for |
acc.tol |
numerical tolerance (relevant only for |
... |
additional arguments to be passed to
|
For type = "orig", essentially the same is calculated
as – for single points – by acceptbin function
from Blaker (2000).
Single values of the “unimodalized” acceptability function
(for type = "unimod") are computed by an iterative
numerical algorithm implemented in internal function
binom.blaker.acc.single.p.
The function cited is called just once in each of the intervals
where the acceptability function is continuous
(namely in the leftmost one of those points of p
that fall into the interval when dealing with points
below x/n, and the rightmost one when above
x/n). The rest is done by function
cummax.
This is considerably faster than calling
binom.blaker.acc.single.p
for every point of p.
Note that applying cummax directly to
a vector of unmodified acceptability values
is even faster and provides a unimodal output;
it may, nevertheless, lack accuracy (see Examples).
Vector of acceptability values (with or without unimodalization)
in points of p.
Inspired by M.P. Fay (2010), mentioning “unavoidable inconsistencies” between tests with non-unimodal acceptability functions and confidence intervals derived from them. When the acceptability functions are unimodalized and the test modified accordingly (i.e. p-values slightly increased in some cases), a perfectly matching test-CI pair is obtained.
Jan Klaschka [email protected]
Blaker, H. (2000) Confidence curves and improved exact confidence
intervals for discrete distributions.
Canadian Journal of Statistics 28: 783-798.
(Corrigenda: Canadian Journal of Statistics 29: 681.)
Fay, M.P. (2010). Two-sided Exact Tests and Matching Confidence Intervals for Discrete Data. R Journal 2(1): 53-58.
p <- seq(0,1,length=1001) acc <- binom.blaker.acc(3,10,p) acc1 <- binom.blaker.acc(3,10,p,type="unimod") ## The two functions look the same at first glance. plot(p,acc,type="l") lines(p,acc1,col="red") legend(x=.7,y=.8,c("orig","unimod"),col=c("black","red"),lwd=1) ## There is, nevertheless, a difference. plot(p,acc1-acc,type="l") ## Focussing on the difference about p=0.4: p <- seq(.395,.405,length=1001) acc <- binom.blaker.acc(3,10,p) acc1 <- binom.blaker.acc(3,10,p,type="unimod") plot(p,acc,type="l",ylim=c(.749,.7495)) lines(p,acc1,col="red") legend(x=.402,y=.7494,c("orig","unimod"),col=c("black","red"),lwd=1) ## Difference between type="unimod" and mere applying ## cummax to values obtained via type="orig": p <- seq(0,1,length=1001) x <- 59 n <- 355 ## Upper confidence limit (at 0.95 level) is slightly above 0.209: binom.blaker.limits(x,n) ## [1] 0.1300807 0.2090809 ## Unmodified acceptability value fall below 0.05 at p = .209 ## left to the limit (so that the null hypothesis p = .209 ## would be rejected despite the fact that p lies within ## the confidence interval): acc <- binom.blaker.acc(59,355,p) rbind(p,acc)[,207:211] ## [,1] [,2] [,3] [,4] [,5] ## p 0.20600000 0.20700000 0.20800000 0.20900000 0.21000000 ## acc 0.06606867 0.05759836 0.05014189 0.04999082 0.04330283 ## ## Modified acceptability is above 0.05 at p = 0.05 (so that ## hypothesis p = 0.05 is not rejected by the modified test): acc1 <- binom.blaker.acc(59,355,p,type="unimod") rbind(p,acc1)[,207:211] ## [,1] [,2] [,3] [,4] [,5] ## p 0.20600000 0.20700000 0.20800000 0.20900000 0.21000000 ## acc1 0.06608755 0.05759836 0.05014189 0.05000009 0.04331409 ## ## Applying cummax to unmodified acceptabilities guarantees unimodality ## but lacks accuracy, leaving the value at p = 0.209 below 0.05: m <- max(which(p <= 59/355)) acc2 <- acc acc2[1:m] <- cummax(acc2[1:m]) acc2[1001:(m+1)] <- cummax(acc2[1001:(m+1)]) rbind(p,acc2)[,207:211] ## [,1] [,2] [,3] [,4] [,5] ## p 0.20600000 0.20700000 0.20800000 0.20900000 0.21000000 ## acc2 0.06606867 0.05759836 0.05014189 0.04999082 0.04330283p <- seq(0,1,length=1001) acc <- binom.blaker.acc(3,10,p) acc1 <- binom.blaker.acc(3,10,p,type="unimod") ## The two functions look the same at first glance. plot(p,acc,type="l") lines(p,acc1,col="red") legend(x=.7,y=.8,c("orig","unimod"),col=c("black","red"),lwd=1) ## There is, nevertheless, a difference. plot(p,acc1-acc,type="l") ## Focussing on the difference about p=0.4: p <- seq(.395,.405,length=1001) acc <- binom.blaker.acc(3,10,p) acc1 <- binom.blaker.acc(3,10,p,type="unimod") plot(p,acc,type="l",ylim=c(.749,.7495)) lines(p,acc1,col="red") legend(x=.402,y=.7494,c("orig","unimod"),col=c("black","red"),lwd=1) ## Difference between type="unimod" and mere applying ## cummax to values obtained via type="orig": p <- seq(0,1,length=1001) x <- 59 n <- 355 ## Upper confidence limit (at 0.95 level) is slightly above 0.209: binom.blaker.limits(x,n) ## [1] 0.1300807 0.2090809 ## Unmodified acceptability value fall below 0.05 at p = .209 ## left to the limit (so that the null hypothesis p = .209 ## would be rejected despite the fact that p lies within ## the confidence interval): acc <- binom.blaker.acc(59,355,p) rbind(p,acc)[,207:211] ## [,1] [,2] [,3] [,4] [,5] ## p 0.20600000 0.20700000 0.20800000 0.20900000 0.21000000 ## acc 0.06606867 0.05759836 0.05014189 0.04999082 0.04330283 ## ## Modified acceptability is above 0.05 at p = 0.05 (so that ## hypothesis p = 0.05 is not rejected by the modified test): acc1 <- binom.blaker.acc(59,355,p,type="unimod") rbind(p,acc1)[,207:211] ## [,1] [,2] [,3] [,4] [,5] ## p 0.20600000 0.20700000 0.20800000 0.20900000 0.21000000 ## acc1 0.06608755 0.05759836 0.05014189 0.05000009 0.04331409 ## ## Applying cummax to unmodified acceptabilities guarantees unimodality ## but lacks accuracy, leaving the value at p = 0.209 below 0.05: m <- max(which(p <= 59/355)) acc2 <- acc acc2[1:m] <- cummax(acc2[1:m]) acc2[1001:(m+1)] <- cummax(acc2[1001:(m+1)]) rbind(p,acc2)[,207:211] ## [,1] [,2] [,3] [,4] [,5] ## p 0.20600000 0.20700000 0.20800000 0.20900000 0.21000000 ## acc2 0.06606867 0.05759836 0.05014189 0.04999082 0.04330283
Fast and accurate calculation of Blaker's binomial confidence limits.
binom.blaker.limits(x, n, level = 0.95, tol = 1e-10, ...)binom.blaker.limits(x, n, level = 0.95, tol = 1e-10, ...)
x |
number of successes. |
n |
number of trials. |
level |
confidence level. |
tol |
numerical tolerance. |
... |
additional arguments to be passed to |
Note that the Blaker's (1 - alpha) confidence interval
is the convex hull of the set C of those points
where the acceptability function (Blaker (2000)) exceeds
level alpha. The original numerical algorithm from
Blaker (2000) is prone, when C is a union
of disjoint intervals, to skipping a short interval
and finding inaccurate over-liberal confidence limits.
Function binom.blaker.limits is, by contrast,
immune from such failures and yields always as
its result the whole confidence interval (Klaschka (2010)).
Length 2 vector – the lower and upper confidence limits.
Package exactci by M. P. Fay includes another algorithm
that calculates Blaker's binomial confidence limits
(see user-level function binom.exact and internal function
exactbinomCI).
It is more sophisticated than the original Blaker's one,
but considerably slower and sometimes less accurate
than that of binom.blaker.limits.
Earlier 2010 versions of the algorithm of binom.blaker.limits
were designed independently of (though already existing)
M.P. Fay's packages exact2x2 and exactci.
Some later modifications, however, have been inspired
by Fay's programs.
Lecoutre & Poitevineau (2014) designed another algorithm
for the calculation of the Blaker's confidence limits.
Despite more abstract theoretical background and broader
scope (not confined to the binomial distribution),
it is closely analogous to that of binom.blaker.limits.
Jan Klaschka [email protected]
Blaker, H. (2000) Confidence curves and improved exact confidence
intervals for discrete distributions.
Canadian Journal of Statistics 28: 783-798.
(Corrigenda: Canadian Journal of Statistics 29: 681.)
Klaschka, J. (2010). BlakerCI: An algorithm and R package for the Blaker's binomial confidence limits calculation. Technical report No. 1099, Institute of Computer Science, Academy of Sciences of the Czech Republic, http://hdl.handle.net/11104/0195722.
Lecoutre, B. & Poitevineau J. (2014). New results for computing Blaker's exact confidence interval limits for usual one-parameter discrete distributions. Communications in Statistics - Simulation and Computation, http://dx.doi.org/10.1080/03610918.2014.911900.
exactci:binom.exact |
One of the options yields Blaker's limits. The algorithm is more sophisti- |
| cated than the original Blaker's one. | |
propCIs:blakerci |
Implementation of the original algorithm from Blaker (2000). |
binGroup:binBlaker |
Another implementation of the same algorithm. |
binom.blaker.limits(3,10) # [1] 0.08726443 0.61941066 ## Example of a failure of the original algorithm: ## Requires PropCIs package. ## Tolerance 1e-4 - default in the Blaker's paper. ## Not run: blakerci(29,99,conf.level=0.95,tolerance=1e-4) ## [1] 0.2096386 0.3923087 ## The correct upper limit should be 0.3929\dots, ## as demonstrated: ## (1) By the same function with a smaller tolerance: blakerci(29,99,conf.level=0.95,tolerance=1e-7) ## [1] 0.2097022 0.3929079 ## (2) By binom.blaker.limits ## (default confidence limit 0.95, default tolerance 1e-10): binom.blaker.limits(29,99) ## [1] 0.2097022 0.3929079 ## (3) By exactbinomCI function from package exactci ## (default confidence level, default tolerance): exactbinomCI(29,99,tsmethod="blaker")[1:2] ## [1] 0.2097 0.3929 ## The same function, smaller tolerance: exactbinomCI(29,99,tsmethod="blaker",tol=1e-8)[1:2] ## [1] 0.2097022 0.3929079 ## Another example of a failure of the original algorithm ## with even as small tolerance as 1e-6: blakerci(59,355,conf.level=0.95,tolerance=1e-4) ## [1] 0.1299899 0.2085809 blakerci(59,355,conf.level=0.95,tolerance=1e-5) ## [1] 0.1300799 0.2085409 blakerci(59,355,conf.level=0.95,tolerance=1e-6) ## [1] 0.1300799 0.2085349 ## Only for tolerance = 1e-7 the result is satisfactory ## and in agreement with binom.blaker.limits: blakerci(59,355,conf.level=0.95,tolerance=1e-7) ## [1] 0.1300807 0.2090809 binom.blaker.limits(59,355) ## [1] 0.1300807 0.2090809 ## End(Not run)binom.blaker.limits(3,10) # [1] 0.08726443 0.61941066 ## Example of a failure of the original algorithm: ## Requires PropCIs package. ## Tolerance 1e-4 - default in the Blaker's paper. ## Not run: blakerci(29,99,conf.level=0.95,tolerance=1e-4) ## [1] 0.2096386 0.3923087 ## The correct upper limit should be 0.3929\dots, ## as demonstrated: ## (1) By the same function with a smaller tolerance: blakerci(29,99,conf.level=0.95,tolerance=1e-7) ## [1] 0.2097022 0.3929079 ## (2) By binom.blaker.limits ## (default confidence limit 0.95, default tolerance 1e-10): binom.blaker.limits(29,99) ## [1] 0.2097022 0.3929079 ## (3) By exactbinomCI function from package exactci ## (default confidence level, default tolerance): exactbinomCI(29,99,tsmethod="blaker")[1:2] ## [1] 0.2097 0.3929 ## The same function, smaller tolerance: exactbinomCI(29,99,tsmethod="blaker",tol=1e-8)[1:2] ## [1] 0.2097022 0.3929079 ## Another example of a failure of the original algorithm ## with even as small tolerance as 1e-6: blakerci(59,355,conf.level=0.95,tolerance=1e-4) ## [1] 0.1299899 0.2085809 blakerci(59,355,conf.level=0.95,tolerance=1e-5) ## [1] 0.1300799 0.2085409 blakerci(59,355,conf.level=0.95,tolerance=1e-6) ## [1] 0.1300799 0.2085349 ## Only for tolerance = 1e-7 the result is satisfactory ## and in agreement with binom.blaker.limits: blakerci(59,355,conf.level=0.95,tolerance=1e-7) ## [1] 0.1300807 0.2090809 binom.blaker.limits(59,355) ## [1] 0.1300807 0.2090809 ## End(Not run)
Calculates values of the Vos-Hudson adjusted acceptability function in a sequence of points (for, e.g., plotting purposes). The adjusted acceptability function may optionally be “unimodalized”, i.e. replaced with the smallest greater or equal unimodal function.
binom.blaker.VHadj.acc(x, n, p, type = c("orig", "unimod"), acc.tol = 1e-10, nmax=n+1000,int.eps=1e-12, ...)binom.blaker.VHadj.acc(x, n, p, type = c("orig", "unimod"), acc.tol = 1e-10, nmax=n+1000,int.eps=1e-12, ...)
x |
number of successes. |
n |
number of trials. |
p |
vector (length 1 allowed) of hypothesized binomial parameters (between 0 and 1). In case of more than one point, an increasing sequence required. |
type |
for |
acc.tol |
numerical tolerance (relevant only for |
nmax |
Pairs |
int.eps |
Maximum expected error of machine representation of integers
calculated from reals via multiplication and division.
(Used in order to round numbers correctly if they happen
to be integer, e. g.
|
... |
additional arguments to be passed to |
The relationship between the adjusted acceptability function
and the adjusted confidence intervals
(see binom.blaker.VHadj.limits)
is the same as between the unadjusted acceptability function
and confidence interval (see binom.blaker.acc,
binom.blaker.limits): The confidence interval is the
convex hull of the set of those points where the function
exceeds 1 - confidence level.
Vector of Vos-Hudson adjusted acceptability values (with or without unimodalization) in points of p.
(1) Comparing output of the function with that of
binom.blaker.acc cannot answer positively the question
whether the unadjusted and adjusted functions are identical
on an interval (but, up to the numerical accuracy, in the points
of p only).
(2) The Warning section of the binom.blaker.VHadj.limits
documentation is relevant here, as well.
Jan Klaschka [email protected]
p <- seq(0,1,length=10001) acc.adj <- binom.blaker.VHadj.acc(6,13,p) acc <- binom.blaker.acc(6,13,p) plot(p,acc.adj,type="l",col="red",ylab="acceptability" ,main=paste("Vos-Hudson adjustment of acceptability function" ,"for 6 successes in 13 trials" , sep="\n") ) lines(p,acc,type="l") legend(x=.7,y=.8,c("unadjusted","adjustment"),col=c("black","red"),lwd=1) ## Plot of differences between the unadjusted and adjusted ## acceptability functions reveals some adjustment details ## hardly visible in the previous graph. plot(p,acc.adj-acc,type="l",ylab="acceptability difference") ## The narrow peak near 0.215 is close to the ## Blaker's lower 0.95 confidence limit. ## ## Focussing on the neighbourhood of 0.215: p <- seq(0.21,0.22,length=1001) acc.adj <- binom.blaker.VHadj.acc(6,13,p) acc <- binom.blaker.acc(6,13,p) plot(p,acc.adj,type="l",col="red",ylab="acceptability" ,main=paste("A detail of Vos-Hudson adjustment of acceptability function" ,"for 6 successes in 13 trials" ,sep="\n") ,ylim=c(0.02,0.09) ) lines(p,acc,type="l") legend(x=.210,y=.08,c("unadjusted","adjustment"),col=c("black","red"),lwd=1) ## The above adjustment results from the fact that, though ## 15 > 13 and 7/15 > 6/13, the acceptability function ## for 7 successes in 15 trials is greater that that for 6 successes ## in 13 trials on a short interval: acc.7.15 <- binom.blaker.acc(7,15,p) plot(p,acc,type="l",ylab="acceptability" ,main=paste("A detail of acceptability functions" ,sep="\n") ,ylim=c(0.02,0.09) ) lines(p,acc.7.15,type="l",col="green") legend(x=.210,y=.08,c("6 / 13","7 / 15"),col=c("black","green") ,title="succ / trials",lwd=1) ## The adjustment shifts the point where the 0.05 level is exceeded, ## i. e. the Blaker's lower 0.95 confidence limit, from 0.2158 to 0.2150. ## (Compare with Examples in binom.blaker.VHadj.limits section.)p <- seq(0,1,length=10001) acc.adj <- binom.blaker.VHadj.acc(6,13,p) acc <- binom.blaker.acc(6,13,p) plot(p,acc.adj,type="l",col="red",ylab="acceptability" ,main=paste("Vos-Hudson adjustment of acceptability function" ,"for 6 successes in 13 trials" , sep="\n") ) lines(p,acc,type="l") legend(x=.7,y=.8,c("unadjusted","adjustment"),col=c("black","red"),lwd=1) ## Plot of differences between the unadjusted and adjusted ## acceptability functions reveals some adjustment details ## hardly visible in the previous graph. plot(p,acc.adj-acc,type="l",ylab="acceptability difference") ## The narrow peak near 0.215 is close to the ## Blaker's lower 0.95 confidence limit. ## ## Focussing on the neighbourhood of 0.215: p <- seq(0.21,0.22,length=1001) acc.adj <- binom.blaker.VHadj.acc(6,13,p) acc <- binom.blaker.acc(6,13,p) plot(p,acc.adj,type="l",col="red",ylab="acceptability" ,main=paste("A detail of Vos-Hudson adjustment of acceptability function" ,"for 6 successes in 13 trials" ,sep="\n") ,ylim=c(0.02,0.09) ) lines(p,acc,type="l") legend(x=.210,y=.08,c("unadjusted","adjustment"),col=c("black","red"),lwd=1) ## The above adjustment results from the fact that, though ## 15 > 13 and 7/15 > 6/13, the acceptability function ## for 7 successes in 15 trials is greater that that for 6 successes ## in 13 trials on a short interval: acc.7.15 <- binom.blaker.acc(7,15,p) plot(p,acc,type="l",ylab="acceptability" ,main=paste("A detail of acceptability functions" ,sep="\n") ,ylim=c(0.02,0.09) ) lines(p,acc.7.15,type="l",col="green") legend(x=.210,y=.08,c("6 / 13","7 / 15"),col=c("black","green") ,title="succ / trials",lwd=1) ## The adjustment shifts the point where the 0.05 level is exceeded, ## i. e. the Blaker's lower 0.95 confidence limit, from 0.2158 to 0.2150. ## (Compare with Examples in binom.blaker.VHadj.limits section.)
Blaker's binomial confidence limits adjusted so that logical inconsistencies criticized by Vos and Hudson (2008) are avoided.
binom.blaker.VHadj.limits(x, n, level = 0.95, tol = 1e-10, ...)binom.blaker.VHadj.limits(x, n, level = 0.95, tol = 1e-10, ...)
x |
number of successes. |
n |
number of trials. |
level |
confidence level. |
tol |
numerical tolerance. |
... |
additional arguments to be passed to |
Length 2 vector – the lower and upper (adjusted) confidence limits.
The stopping rule used is not fully justified:
The Clopper-Pearson 1 - alpha confidence bounds
for x successes in n trials
may be expressed as qbeta(alpha/2,x,n-x+1) and
qbeta(1-alpha/2,x+1,n-x),
and can be generalized this way to real
(i. e. not only integer) values of x.
The stopping rule used in binom.blaker.VHadj.limits
relies on the hypothesis that
the generalized lower (upper) Clopper-Pearson confidence bounds
grow (decrease) whenever the number of trials grows,
and the proportion of successes grows (decreases) or
remains unchanged (with obvious exceptions in extremes).
Though I firmly trust the hypothesis, I can prove it, so far,
just for integer numbers of successes (i. e. for “ordinary”
Clopper-Pearson confidence bounds, not the generalized ones),
and lack a general proof.
Should the hypothesis be invalid, the stopping rule
implemented in binom.blaker.VHadj.limits
would be incorrect, and the process of modifying
the Blaker's confidence bounds could be incomplete
in some cases.
Vos & Hudson (2008) gave examples of mutually contradictory
inferences yielded by some binomial tests and confidence
intervals, including the Blaker's confidence interval.
Their objections may be interpreted as follows:
When the number of trials is increased so that the success
proportion increases (decreases) or remains the same,
the lower (upper) confidence limit at the same confidence level
should not decrease (increase).
The adjustment implemented in binom.blaker.VHadj.limits
replaces the lower (upper) Blaker's confidence limit
for x successes in n trials
with the infimum (supremum) of the Blaker's lower (upper)
confidence limits over such pairs y, m
that m is not less that n, and
y/m is not less (greater) than x/n.
Note that Lecoutre & Poitevineau (2014), refering to the
criticism by
Vos & Hudson, proposed a modification of the Blaker's
confidence limits.
Their adjustment, however, eliminates only a subset of
“discrepancies” treated by binom.blaker.VHadj.limits,
namely nonmonotonicities of upper (lower) Blaker's confidence
bounds in the number of trials when the number of successes
(failures) remains the same.
Jan Klaschka [email protected]
Vos, P. W. & Hudson, S. (2008). Problems with binomial two-sided tests and the associated confidence intervals. Australian & New Zealand Journal of Statistics 50(1): 81-89.
Lecoutre, B. & Poitevineau, J. (2014). New results for computing Blaker's exact confidence interval limits for usual one-parameter discrete distributions. Communications in Statistics - Simulation and Computation, http://dx.doi.org/10.1080/03610918.2014.911900.
binom.blaker.VHadj.limits(6,13) # [1] 0.2150187 0.7395922 ## Note that the lower limit differs from the ## unadjusted version: binom.blaker.limits(6,13) # [1] 0.2158050 0.7395922 ## The (unadjusted) lower limit was replaced with the ## Blaker's lower limit (both unadjusted and adjusted) ## assigned to 7 successes in 15 trials: binom.blaker.limits(7,15) # [1] 0.2150187 0.7096627 binom.blaker.VHadj.limits(7,15) # [1] 0.2150187 0.7096627 ## The adjustment avoids a contradiction between ## inferences corresponding to ## 6 successes in 13 trials, and 7 successess in 15 trials: ## Though the latter situation means a higher succes proportion ## in a higher number of trials, it is assigned a smaller ## (unadjusted) Blaker's 95% lower confidence limit.binom.blaker.VHadj.limits(6,13) # [1] 0.2150187 0.7395922 ## Note that the lower limit differs from the ## unadjusted version: binom.blaker.limits(6,13) # [1] 0.2158050 0.7395922 ## The (unadjusted) lower limit was replaced with the ## Blaker's lower limit (both unadjusted and adjusted) ## assigned to 7 successes in 15 trials: binom.blaker.limits(7,15) # [1] 0.2150187 0.7096627 binom.blaker.VHadj.limits(7,15) # [1] 0.2150187 0.7096627 ## The adjustment avoids a contradiction between ## inferences corresponding to ## 6 successes in 13 trials, and 7 successess in 15 trials: ## Though the latter situation means a higher succes proportion ## in a higher number of trials, it is assigned a smaller ## (unadjusted) Blaker's 95% lower confidence limit.
For binomial distribution:
Calculation of the lower Blaker's confidence limit
as defined by Blaker (binom.blaker.lower.limit),
or with so called Vos-Hudson adjustment (binom.blaker.VHadj.lower.limit);
a single acceptability value, optionally “unimodalized”
(binom.blaker.acc.single.p).
For Poisson distribution:
Calculation of the lower and upper Blaker's confidence limits
(poisson.blaker.lower.limit, poisson.blaker.upper.limit);
a single acceptability value, optionally “unimodalized”
(poisson.blaker.acc.single.p).
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) poisson.blaker.lower.limit(x, level, tol = 1e-10, maxiter=100) poisson.blaker.upper.limit(x, level, tol = 1e-10, maxiter=100) poisson.blaker.acc.single.p(x, p, type = "orig", acc.tol = 1e-10, output = "acc", maxiter=100)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) poisson.blaker.lower.limit(x, level, tol = 1e-10, maxiter=100) poisson.blaker.upper.limit(x, level, tol = 1e-10, maxiter=100) poisson.blaker.acc.single.p(x, p, type = "orig", acc.tol = 1e-10, output = "acc", maxiter=100)
x |
number of successes (binomial case), or events (Poisson case). |
n |
number of trials. |
level |
confidence level. |
tol |
numerical tolerance (for the confidence limit). |
p |
point (binomial or Poisson parameter value) where to calculate the acceptability. |
type |
|
acc.tol |
numerical tolerance (for the acceptability values when |
output |
the acceptability value output ( |
maxiter |
Maximum number of interval halving iterations during the search
for a confidence limit ( |
nmax |
Pairs |
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.
|
For binom.blaker.lower.limit and
binom.blaker.VHadj.lower.limit, a single number –
the lower confidence limit.
For binom.blaker.acc.single.p – depending on the
output parameter – a single acceptability value, or a single
auxiliary integer, or both.
Jan Klaschka [email protected]
binom.blaker.limits, binom.blaker.VHadj.limits,binom.blaker.acc, binom.blaker.VHadj.acc,
poisson.blaker.limits, poisson.blaker.acc.
Calculates values of the acceptability function for the Poisson distribution (see Blaker (2000)) in a sequence of points (for, e.g., plotting purposes). The acceptability function may optionally be “unimodalized”, i.e. replaced with the smallest greater or equal unimodal function.
poisson.blaker.acc(x, p, type = c("orig", "unimod"), acc.tol = 1e-10, ...)poisson.blaker.acc(x, p, type = c("orig", "unimod"), acc.tol = 1e-10, ...)
x |
number of events. |
p |
vector (length 1 allowed) of hypothesized Poisson parameters. In case of more than one point, an increasing sequence required. |
type |
for |
acc.tol |
numerical tolerance (relevant only for |
... |
additional arguments to be passed to
|
Single values of the “unimodalized” acceptability function
(for type = "unimod") are computed by an iterative
numerical algorithm implemented in internal function
poisson.blaker.acc.single.p.
The function cited is called just once in each of the intervals
where the acceptability function is continuous
(namely in the leftmost one of those points of p
that fall into the interval when dealing with points
below x, and the rightmost one when above
x). The rest is done by function
cummax.
This is considerably faster than calling
poisson.blaker.acc.single.p
for every point of p.
Note that applying cummax directly to
a vector of unmodified acceptability values
is even faster and provides a unimodal output;
it may, nevertheless, lack accuracy.
Vector of acceptability values (with or without unimodalization)
in points of p.
Inspired by M.P. Fay (2010), mentioning “unavoidable inconsistencies” between tests with non-unimodal acceptability functions and confidence intervals derived from them. When the acceptability functions are unimodalized and the test modified accordingly (i.e. p-values slightly increased in some cases), a perfectly matching test-CI pair is obtained.
Jan Klaschka [email protected]
Blaker, H. (2000) Confidence curves and improved exact confidence
intervals for discrete distributions.
Canadian Journal of Statistics 28: 783-798.
(Corrigenda: Canadian Journal of Statistics 29: 681.)
Fay, M.P. (2010). Two-sided Exact Tests and Matching Confidence Intervals for Discrete Data. R Journal 2(1): 53-58.
p <- seq(0,10,length=1001) acc <- poisson.blaker.acc(3,p) acc1 <- poisson.blaker.acc(3,p,type="unimod") plot(p,acc,type="l") lines(p,acc1,col="red") legend(x=7,y=.8,c("orig","unimod"),col=c("black","red"),lwd=1) ## The two lines -- the unimodalized and original acceptabilities -- ## look almost the same but some small differences are slightly ## visible. ## They can be seen better this way: plot(p,acc1-acc,type="l") ## Focussing on one of them: p <- seq(5.05,5.6,length=1001) acc <- poisson.blaker.acc(3,p) acc1 <- poisson.blaker.acc(3,p,type="unimod") plot(p,acc,type="l",ylim=c(.391,.396)) lines(p,acc1,col="red") legend(x=5.4,y=.395,c("orig","unimod"),col=c("black","red"),lwd=1)p <- seq(0,10,length=1001) acc <- poisson.blaker.acc(3,p) acc1 <- poisson.blaker.acc(3,p,type="unimod") plot(p,acc,type="l") lines(p,acc1,col="red") legend(x=7,y=.8,c("orig","unimod"),col=c("black","red"),lwd=1) ## The two lines -- the unimodalized and original acceptabilities -- ## look almost the same but some small differences are slightly ## visible. ## They can be seen better this way: plot(p,acc1-acc,type="l") ## Focussing on one of them: p <- seq(5.05,5.6,length=1001) acc <- poisson.blaker.acc(3,p) acc1 <- poisson.blaker.acc(3,p,type="unimod") plot(p,acc,type="l",ylim=c(.391,.396)) lines(p,acc1,col="red") legend(x=5.4,y=.395,c("orig","unimod"),col=c("black","red"),lwd=1)
Fast and accurate calculation of Blaker's Poisson confidence limits.
poisson.blaker.limits(x, level = 0.95, tol = 1e-10, ...)poisson.blaker.limits(x, level = 0.95, tol = 1e-10, ...)
x |
number of events. |
level |
confidence level. |
tol |
numerical tolerance. |
... |
additional arguments to be passed to |
Note that the Blaker's (1 - alpha) confidence interval
is the convex hull of the set C of those points
where the acceptability function (Blaker (2000)) exceeds
level alpha.
When C is not connected, the algorithm is, analogously to
binom.blaker.limits (see its details),
immune from leaving out short intervals and making thus
the confidence intervals over-liberal.
Length 2 vector – the lower and upper confidence limits.
Package exactci by M. P. Fay includes another algorithm
that calculates Blaker's Poisson confidence limits
(see user-level function poisson.exact and internal function
exactpoissonCI).
Lecoutre & Poitevineau (2014) designed another algorithm
for the calculation of the Blaker's confidence limits.
It is closely analogous to that of poisson.blaker.limits.
Jan Klaschka [email protected]
Blaker, H. (2000) Confidence curves and improved exact confidence
intervals for discrete distributions.
Canadian Journal of Statistics 28: 783-798.
(Corrigenda: Canadian Journal of Statistics 29: 681.)
Lecoutre, B. & Poitevineau J. (2014). New results for computing Blaker's exact confidence interval limits for usual one-parameter discrete distributions. Communications in Statistics - Simulation and Computation, http://dx.doi.org/10.1080/03610918.2014.911900.
exactci:poisson.exact |
One of the options yields Blaker's limits. |
poisson.blaker.limits(3) # [1] 0.8176914 8.5597971poisson.blaker.limits(3) # [1] 0.8176914 8.5597971