R help - Jan 2011 - median by geometric mean -- are we missing what's important?

Folks:

I know this may be overreaching, but are we missing what's important?
WHY do the zeros occur? Are they values less then a known or unknown
LOD? -- and/or is there positive mass on zero? In either case, using
logs to calculate a geometric mean may not make sense. Paraphrasing
Greg Snow, what is the scientific question? What is the model?

Cheers,
Bert



On Mon, Jan 17, 2011 at 9:13 AM, Keith Jewell <k.jewell at campden.co.uk>
wrote:
> Just in case some of x are negative (the desired median still exists, as
> long as the two middle values are non -ve), how about:
>
> x <- runif(20, -1, 100)
> exp(median(log(pmax(0,x))))
>
> It'll give -Inf if the two middle values are negative, when I guess we
> should get NaN, but I can't see a 1-line way to handle that!
>
> Keith J
>
> "Peter Ehlers" <ehlers at ucalgary.ca> wrote in message
> news:4D3468EF.5010601 at ucalgary.ca...
>> I've been reminded by Prof. Brian Ripley that R's
>> log() function will indeed handle zeros appropriately.
>>
>> Apologies to S Ellison and Hadley Wickham.
>>
>> Peter Ehlers
>>
>> On 2011-01-17 06:55, Peter Ehlers wrote:
>>> On 2011-01-17 02:19, S Ellison wrote:
>>>> Will this do?
>>>>
>>>> x<- runif(20, 1, 100)
>>>>
>>>> exp( median( log( x) ) )
>>>>
>>>> S Ellison
>>>>
>>>>
>>> That's what Hadley proposed, too. It's fine for
>>> your example, but there is potentially a small
>>> problem with this method: the data must be positive.
>>> Since it's not unusual to see data with some zeros,
>>> the log() would fail.
>>>
>>> Depending on what type of data I was going to use
>>> this modification of the median for, I would consider
>>> modifying the (quite short) median.default function,
>>> with appropriate additional data checks.
>>>
>>> Peter Ehlers
>>>
>>>>
>>>>>>> Skull Crossbones<witch.of.agnessi at
gmail.com> ? 15/01/2011 16:26>>>
>>>> Hi All,
>>>>
>>>> I need to calculate the median for even number of data
points.However
>>>> instead of calculating
>>>> the arithmetic mean of the two middle values,I need to
calculate their
>>>> geometric mean.
>>>>
>>>> Though I can code this in R, possibly in a few lines, but
wondering if
>>>> there
>>>> is
>>>> already some built in function.
>>>>
>>>> Can somebody give a hint?
>>>>
>>>> Thanks in advance
>>>>
>>
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
>


-- 
Bert Gunter
Genentech Nonclinical Biostatistics

On Mon, Jan 17, 2011 at 9:23 AM, Bert Gunter <gunter.berton at gene.com>
wrote:
> Folks:
>
> I know this may be overreaching, but are we missing what's important?
> WHY do the zeros occur? Are they values less then a known or unknown
> LOD? -- and/or is there positive mass on zero? In either case, using
> logs to calculate a geometric mean may not make sense. Paraphrasing
Isn't this a bit of a general problem with the geometric mean if there
are 0s or an odd number of negative numbers it becomes 0 or imaginary
(please do correct me if I'm wrong)?

sqrt(prod(c(2, 0, 54)))
sqrt(prod(c(-2, 2)))

> Greg Snow, what is the scientific question? What is the model?
>
> Cheers,
> Bert
>
>
>
> On Mon, Jan 17, 2011 at 9:13 AM, Keith Jewell <k.jewell at
campden.co.uk> wrote:
>> Just in case some of x are negative (the desired median still exists,
as
>> long as the two middle values are non -ve), how about:
>>
>> x <- runif(20, -1, 100)
>> exp(median(log(pmax(0,x))))
>>
>> It'll give -Inf if the two middle values are negative, when I guess
we
>> should get NaN, but I can't see a 1-line way to handle that!
>>
>> Keith J
>>
>> "Peter Ehlers" <ehlers at ucalgary.ca> wrote in message
>> news:4D3468EF.5010601 at ucalgary.ca...
>>> I've been reminded by Prof. Brian Ripley that R's
>>> log() function will indeed handle zeros appropriately.
>>>
>>> Apologies to S Ellison and Hadley Wickham.
>>>
>>> Peter Ehlers
>>>
>>> On 2011-01-17 06:55, Peter Ehlers wrote:
>>>> On 2011-01-17 02:19, S Ellison wrote:
>>>>> Will this do?
>>>>>
>>>>> x<- runif(20, 1, 100)
>>>>>
>>>>> exp( median( log( x) ) )
>>>>>
>>>>> S Ellison
>>>>>
>>>>>
>>>> That's what Hadley proposed, too. It's fine for
>>>> your example, but there is potentially a small
>>>> problem with this method: the data must be positive.
>>>> Since it's not unusual to see data with some zeros,
>>>> the log() would fail.
>>>>
>>>> Depending on what type of data I was going to use
>>>> this modification of the median for, I would consider
>>>> modifying the (quite short) median.default function,
>>>> with appropriate additional data checks.
>>>>
>>>> Peter Ehlers
>>>>
>>>>>
>>>>>>>> Skull Crossbones<witch.of.agnessi at
gmail.com> ? 15/01/2011 16:26>>>
>>>>> Hi All,
>>>>>
>>>>> I need to calculate the median for even number of data
points.However
>>>>> instead of calculating
>>>>> the arithmetic mean of the two middle values,I need to
calculate their
>>>>> geometric mean.
>>>>>
>>>>> Though I can code this in R, possibly in a few lines, but
wondering if
>>>>> there
>>>>> is
>>>>> already some built in function.
>>>>>
>>>>> Can somebody give a hint?
>>>>>
>>>>> Thanks in advance
>>>>>
>>>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> 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.
>>
>
>
>
> --
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
>


-- 
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/