[R] median by geometric mean -- are we missing what's important?

[Joshua Wiley]

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
>>>>>
>>>
>>
>> ______________________________________________
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>> 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/