Question on Binom.Confint

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Question on Binom.Confint

Guo, Fang (Associate)
Hi,

I have a question with the function Binom.Confint(x,n,"method"=lrt). For likelihood ratio test, I'd like to ask how you define the upper limit when the frequency of successes is zero. Thanks!


Fang Guo
Associate

CORNERSTONE RESEARCH
699 Boylston Street, 5th Floor
Boston, MA 02116-2836
617.927.3042 direct
[hidden email]<mailto:[hidden email]>

www.cornerstone.com<http://www.cornerstone.com/>


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Re: Question on Binom.Confint

David Winsemius

> On Sep 13, 2018, at 1:15 PM, Guo, Fang (Associate) <[hidden email]> wrote:
>
> Hi,
>
> I have a question with the function Binom.Confint(x,n,"method"=lrt). For likelihood ratio test, I'd like to ask how you define the upper limit when the frequency of successes is zero. Thanks!

First you need to tell use where you are getting Binom.Confint.

Error: object 'Binom.Confint' not found

--
David,

>
>
> Fang Guo
> Associate
>
> CORNERSTONE RESEARCH
> 699 Boylston Street, 5th Floor
> Boston, MA 02116-2836
> 617.927.3042 direct
> [hidden email]<mailto:[hidden email]>
>
> www.cornerstone.com<http://www.cornerstone.com/>
>
>
> ***********************************************************
> Warning: This email may contain confidential or privileged information
> intended only for the use of the individual or entity to whom it is
> addressed. If you are not the intended recipient, please understand
> that any disclosure, copying, distribution, or use of the contents
> of this email is strictly prohibited.
> ***********************************************************
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law

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Re: [FORGED] Question on Binom.Confint

Rolf Turner
In reply to this post by Guo, Fang (Associate)

On 09/14/2018 08:15 AM, Guo, Fang (Associate) wrote:

> Hi,
>
> I have a question with the function Binom.Confint(x,n,"method"=lrt).
> For likelihood ratio test, I'd like to ask how you define the upper
> limit when the frequency of successes is zero. Thanks!

Point 1:  This question is inappropriate for this list, since it is
about statistical theory and not about R syntax and programming.

Point 2: Where did you find the function Binom.Confint()?  I can find no
such function anywhere.  I did manage to locate a function
binom.confint() (note the lower case "b" and "c") but it does not have
an argument "method".  Please do not expect those whom you are
addressing to be telepathic.

Point 3:  Having "method"=lrt in the call is decidedly weird.  Perhaps
you meant method="lrt"; this is entirely different.

cheers,

Rolf Turner

--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

______________________________________________
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Re: Question on Binom.Confint

Bert Gunter-2
In reply to this post by Guo, Fang (Associate)
In what package?
Binomial confidence interval functions are in several.

Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Thu, Sep 13, 2018 at 6:38 PM Guo, Fang (Associate)
<[hidden email]> wrote:

>
> Hi,
>
> I have a question with the function Binom.Confint(x,n,"method"=lrt). For likelihood ratio test, I'd like to ask how you define the upper limit when the frequency of successes is zero. Thanks!
>
>
> Fang Guo
> Associate
>
> CORNERSTONE RESEARCH
> 699 Boylston Street, 5th Floor
> Boston, MA 02116-2836
> 617.927.3042 direct
> [hidden email]<mailto:[hidden email]>
>
> www.cornerstone.com<http://www.cornerstone.com/>
>
>
> ***********************************************************
> Warning: This email may contain confidential or privileged information
> intended only for the use of the individual or entity to whom it is
> addressed. If you are not the intended recipient, please understand
> that any disclosure, copying, distribution, or use of the contents
> of this email is strictly prohibited.
> ***********************************************************
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Question on Binom.Confint

Spencer Graves-4
In reply to this post by David Winsemius


On 2018-09-13 20:58, David Winsemius wrote:
>> On Sep 13, 2018, at 1:15 PM, Guo, Fang (Associate) <[hidden email]> wrote:
>>
>> Hi,
>>
>> I have a question with the function Binom.Confint(x,n,"method"=lrt). For likelihood ratio test, I'd like to ask how you define the upper limit when the frequency of successes is zero. Thanks!
> First you need to tell use where you are getting Binom.Confint.
>
> Error: object 'Binom.Confint' not found
>

       sos::findFn('Binom.Confint') found NO function named
"Binom.Confint", but it did find two named "binom.confint", one in the
"binom" package and the other in the "NNTbiomarker" package. The same
search in "rdocumentation.org" returned the same results. The indicated
command would not work in either.


       Spencer

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Re: Question on Binom.Confint

Jim Lemon-4
In reply to this post by Guo, Fang (Associate)
Hi Fang,
Let's assume that you are using the "binom.confint" function in the
"binom" package and you have made a spelling mistake or two. This
function employs nine methods for estimating the binomial confidence
interval. Sadly, none of these is "lrt". The zero condition is
discussed in the help page for four of these methods. Assuming you
want to use another method, you will have to look up the method. A
good start is:

https://en.wikipedia.org/wiki/Binomial_proportion_confidence_interval

Jim

On Fri, Sep 14, 2018 at 11:38 AM Guo, Fang (Associate)
<[hidden email]> wrote:

>
> Hi,
>
> I have a question with the function Binom.Confint(x,n,"method"=lrt). For likelihood ratio test, I'd like to ask how you define the upper limit when the frequency of successes is zero. Thanks!
>
>
> Fang Guo
> Associate
>
> CORNERSTONE RESEARCH
> 699 Boylston Street, 5th Floor
> Boston, MA 02116-2836
> 617.927.3042 direct
> [hidden email]<mailto:[hidden email]>
>
> www.cornerstone.com<http://www.cornerstone.com/>
>
>
> ***********************************************************
> Warning: This email may contain confidential or privileged information
> intended only for the use of the individual or entity to whom it is
> addressed. If you are not the intended recipient, please understand
> that any disclosure, copying, distribution, or use of the contents
> of this email is strictly prohibited.
> ***********************************************************
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [FORGED] Question on Binom.Confint

Guo, Fang (Associate)
In reply to this post by Rolf Turner
It's method="lrt" and I used the "binom" package.

-----Original Message-----
From: Rolf Turner [mailto:[hidden email]]
Sent: Thursday, September 13, 2018 10:02 PM
To: Guo, Fang (Associate) <[hidden email]>
Cc: [hidden email]
Subject: Re: [FORGED] [R] Question on Binom.Confint


On 09/14/2018 08:15 AM, Guo, Fang (Associate) wrote:

> Hi,
>
> I have a question with the function Binom.Confint(x,n,"method"=lrt).
> For likelihood ratio test, I'd like to ask how you define the upper
> limit when the frequency of successes is zero. Thanks!

Point 1:  This question is inappropriate for this list, since it is about statistical theory and not about R syntax and programming.

Point 2: Where did you find the function Binom.Confint()?  I can find no such function anywhere.  I did manage to locate a function
binom.confint() (note the lower case "b" and "c") but it does not have an argument "method".  Please do not expect those whom you are addressing to be telepathic.

Point 3:  Having "method"=lrt in the call is decidedly weird.  Perhaps you meant method="lrt"; this is entirely different.

cheers,

Rolf Turner

--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
***********************************************************
Warning: This email may contain confidential or privileged information
intended only for the use of the individual or entity to whom it is
addressed. If you are not the intended recipient, please understand
that any disclosure, copying, distribution, or use of the contents
of this email is strictly prohibited.
***********************************************************
______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Question on Binom.Confint

Guo, Fang (Associate)
In reply to this post by Bert Gunter-2
I used library(binom).

-----Original Message-----
From: Bert Gunter [mailto:[hidden email]]
Sent: Thursday, September 13, 2018 10:04 PM
To: Guo, Fang (Associate) <[hidden email]>
Cc: [hidden email]; R-help <[hidden email]>
Subject: Re: [R] Question on Binom.Confint

In what package?
Binomial confidence interval functions are in several.

Bert Gunter

"The trouble with having an open mind is that people keep coming along and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Thu, Sep 13, 2018 at 6:38 PM Guo, Fang (Associate) <[hidden email]> wrote:

>
> Hi,
>
> I have a question with the function Binom.Confint(x,n,"method"=lrt). For likelihood ratio test, I'd like to ask how you define the upper limit when the frequency of successes is zero. Thanks!
>
>
> Fang Guo
> Associate
>
> CORNERSTONE RESEARCH
> 699 Boylston Street, 5th Floor
> Boston, MA 02116-2836
> 617.927.3042 direct
> [hidden email]<mailto:[hidden email]>
>
> www.cornerstone.com<http://www.cornerstone.com/>
>
>
> ***********************************************************
> Warning: This email may contain confidential or privileged information
> intended only for the use of the individual or entity to whom it is
> addressed. If you are not the intended recipient, please understand
> that any disclosure, copying, distribution, or use of the contents of
> this email is strictly prohibited.
> ***********************************************************
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
***********************************************************
Warning: This email may contain confidential or privileged information
intended only for the use of the individual or entity to whom it is
addressed. If you are not the intended recipient, please understand
that any disclosure, copying, distribution, or use of the contents
of this email is strictly prohibited.
***********************************************************
______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
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Re: Question on Binom.Confint

Bert Gunter-2
Then it's binom.confint (case matters in R -- PLEASE DO A TUTORIAL OR
TWO!) and there is no "lrt"  option. So no idea what you're referring
to.

-- Bert


On Fri, Sep 14, 2018 at 6:53 AM Guo, Fang (Associate)
<[hidden email]> wrote:

>
> I used library(binom).
>
> -----Original Message-----
> From: Bert Gunter [mailto:[hidden email]]
> Sent: Thursday, September 13, 2018 10:04 PM
> To: Guo, Fang (Associate) <[hidden email]>
> Cc: [hidden email]; R-help <[hidden email]>
> Subject: Re: [R] Question on Binom.Confint
>
> In what package?
> Binomial confidence interval functions are in several.
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
> On Thu, Sep 13, 2018 at 6:38 PM Guo, Fang (Associate) <[hidden email]> wrote:
> >
> > Hi,
> >
> > I have a question with the function Binom.Confint(x,n,"method"=lrt). For likelihood ratio test, I'd like to ask how you define the upper limit when the frequency of successes is zero. Thanks!
> >
> >
> > Fang Guo
> > Associate
> >
> > CORNERSTONE RESEARCH
> > 699 Boylston Street, 5th Floor
> > Boston, MA 02116-2836
> > 617.927.3042 direct
> > [hidden email]<mailto:[hidden email]>
> >
> > www.cornerstone.com<http://www.cornerstone.com/>
> >
> >
> > ***********************************************************
> > Warning: This email may contain confidential or privileged information
> > intended only for the use of the individual or entity to whom it is
> > addressed. If you are not the intended recipient, please understand
> > that any disclosure, copying, distribution, or use of the contents of
> > this email is strictly prohibited.
> > ***********************************************************
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> ***********************************************************
> Warning: This email may contain confidential or privileged information
> intended only for the use of the individual or entity to whom it is
> addressed. If you are not the intended recipient, please understand
> that any disclosure, copying, distribution, or use of the contents
> of this email is strictly prohibited.
> ***********************************************************

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Question on Binom.Confint

Guo, Fang (Associate)
In reply to this post by Jim Lemon-4
I did use library(binom). However, I was able to use the method "lrt" which is short for likelihood ratio test.
-----Original Message-----
From: Jim Lemon [mailto:[hidden email]]
Sent: Thursday, September 13, 2018 11:50 PM
To: Guo, Fang (Associate) <[hidden email]>; r-help mailing list <[hidden email]>
Subject: Re: [R] Question on Binom.Confint

Hi Fang,
Let's assume that you are using the "binom.confint" function in the "binom" package and you have made a spelling mistake or two. This function employs nine methods for estimating the binomial confidence interval. Sadly, none of these is "lrt". The zero condition is discussed in the help page for four of these methods. Assuming you want to use another method, you will have to look up the method. A good start is:

https://en.wikipedia.org/wiki/Binomial_proportion_confidence_interval

Jim

On Fri, Sep 14, 2018 at 11:38 AM Guo, Fang (Associate) <[hidden email]> wrote:

>
> Hi,
>
> I have a question with the function Binom.Confint(x,n,"method"=lrt). For likelihood ratio test, I'd like to ask how you define the upper limit when the frequency of successes is zero. Thanks!
>
>
> Fang Guo
> Associate
>
> CORNERSTONE RESEARCH
> 699 Boylston Street, 5th Floor
> Boston, MA 02116-2836
> 617.927.3042 direct
> [hidden email]<mailto:[hidden email]>
>
> www.cornerstone.com<http://www.cornerstone.com/>
>
>
> ***********************************************************
> Warning: This email may contain confidential or privileged information
> intended only for the use of the individual or entity to whom it is
> addressed. If you are not the intended recipient, please understand
> that any disclosure, copying, distribution, or use of the contents of
> this email is strictly prohibited.
> ***********************************************************
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
***********************************************************
Warning: This email may contain confidential or privileged information
intended only for the use of the individual or entity to whom it is
addressed. If you are not the intended recipient, please understand
that any disclosure, copying, distribution, or use of the contents
of this email is strictly prohibited.
***********************************************************
______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Question on Binom.Confint

Göran Broström-3


On 2018-09-14 17:04, Guo, Fang (Associate) wrote:
> I did use library(binom). However, I was able to use the method "lrt" which is short for likelihood ratio test.

You are right, there is a method "lrt", but it is not mentioned in the
documentation. (Look at the code.)

Göran

> -----Original Message-----
> From: Jim Lemon [mailto:[hidden email]]
> Sent: Thursday, September 13, 2018 11:50 PM
> To: Guo, Fang (Associate) <[hidden email]>; r-help mailing list <[hidden email]>
> Subject: Re: [R] Question on Binom.Confint
>
> Hi Fang,
> Let's assume that you are using the "binom.confint" function in the "binom" package and you have made a spelling mistake or two. This function employs nine methods for estimating the binomial confidence interval. Sadly, none of these is "lrt". The zero condition is discussed in the help page for four of these methods. Assuming you want to use another method, you will have to look up the method. A good start is:
>
> https://en.wikipedia.org/wiki/Binomial_proportion_confidence_interval
>
> Jim
>
> On Fri, Sep 14, 2018 at 11:38 AM Guo, Fang (Associate) <[hidden email]> wrote:
>>
>> Hi,
>>
>> I have a question with the function Binom.Confint(x,n,"method"=lrt). For likelihood ratio test, I'd like to ask how you define the upper limit when the frequency of successes is zero. Thanks!
>>
>>
>> Fang Guo
>> Associate
>>
>> CORNERSTONE RESEARCH
>> 699 Boylston Street, 5th Floor
>> Boston, MA 02116-2836
>> 617.927.3042 direct
>> [hidden email]<mailto:[hidden email]>
>>
>> www.cornerstone.com<http://www.cornerstone.com/>
>>
>>
>> ***********************************************************
>> Warning: This email may contain confidential or privileged information
>> intended only for the use of the individual or entity to whom it is
>> addressed. If you are not the intended recipient, please understand
>> that any disclosure, copying, distribution, or use of the contents of
>> this email is strictly prohibited.
>> ***********************************************************
>>
>>          [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> ***********************************************************
> Warning: This email may contain confidential or privileged information
> intended only for the use of the individual or entity to whom it is
> addressed. If you are not the intended recipient, please understand
> that any disclosure, copying, distribution, or use of the contents
> of this email is strictly prohibited.
> ***********************************************************
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

______________________________________________
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Re: [FORGED] Question on Binom.Confint

Spencer Graves-4
In reply to this post by Guo, Fang (Associate)


On 2018-09-14 08:52, Guo, Fang (Associate) wrote:
> It's method="lrt" and I used the "binom" package.


       The ultimate answer can be obtained as follows:


 > debug(binom.confint)
 > binom.confint(x = 0, n = 100, tol = 1e-8, method='lrt')


       Then walk through the code line by line.


       Reading the code, I find the following:


   if (any(method == "lrt") || all.methods) {
         res.lrt <- binom.lrt(x, n, conf.level = conf.level, ...)
         res <- if (is.null(res))
             res.lrt
         else rbind(res, res.lrt)
     }


       Then check the help page for "binom.lrt".  That includes the
following:


Confidence intervals are based on profiling the binomial deviance in the
neighbourhood of the MLE. If x == 0 or x == n and bayes is TRUE, then a
Bayesian adjustment is made to move the log-likelihood function away
from Inf. Specifically, these values are replaced by (x + 0.5)/(n + 1),
which is the posterier mode of f(p|x) using Jeffrey's prior on p.
Furthermore, if conf.adj is TRUE, then the upper (or lower) bound uses a
1 - alpha confidence level. Typically, the observed mean will not be
inside the estimated confidence interval. If bayes is FALSE, then the
Clopper-Pearson exact method is used on the endpoints. This tends to
make confidence intervals at the end too conservative, though the
observed mean is guaranteed to be within the estimated confidence limits.


       Spencer

>
> -----Original Message-----
> From: Rolf Turner [mailto:[hidden email]]
> Sent: Thursday, September 13, 2018 10:02 PM
> To: Guo, Fang (Associate) <[hidden email]>
> Cc: [hidden email]
> Subject: Re: [FORGED] [R] Question on Binom.Confint
>
>
> On 09/14/2018 08:15 AM, Guo, Fang (Associate) wrote:
>
>> Hi,
>>
>> I have a question with the function Binom.Confint(x,n,"method"=lrt).
>> For likelihood ratio test, I'd like to ask how you define the upper
>> limit when the frequency of successes is zero. Thanks!
> Point 1:  This question is inappropriate for this list, since it is about statistical theory and not about R syntax and programming.
>
> Point 2: Where did you find the function Binom.Confint()?  I can find no such function anywhere.  I did manage to locate a function
> binom.confint() (note the lower case "b" and "c") but it does not have an argument "method".  Please do not expect those whom you are addressing to be telepathic.
>
> Point 3:  Having "method"=lrt in the call is decidedly weird.  Perhaps you meant method="lrt"; this is entirely different.
>
> cheers,
>
> Rolf Turner
>
> --
> Technical Editor ANZJS
> Department of Statistics
> University of Auckland
> Phone: +64-9-373-7599 ext. 88276
> ***********************************************************
> Warning: This email may contain confidential or privileged information
> intended only for the use of the individual or entity to whom it is
> addressed. If you are not the intended recipient, please understand
> that any disclosure, copying, distribution, or use of the contents
> of this email is strictly prohibited.
> ***********************************************************
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.