[R-sig-eco] T50 or ED50 for count data

[Mehdi Abedi]

Dear Tom,
Thanks for your kind reply.
Could we calculate T50 in gamm4 and lme4 as well?
I searched in survival but no special information about median term in the
package survival.

Warm regards,
Mehdi

On Fri, Jul 24, 2015 at 4:11 AM, Philippi, Tom <tom_philippi at nps.gov> wrote:

> Mehdi--
> Based on the example datasets germination and chickweed, drc would work
> with you using the final count of emergence as the number of seeds at risk
> of germinating.  If you get a satisfactory fit from one of the 6 or so
> function forms it supports for dose-response, you may be fine.  [I have
> scientific qualms about treating time as a dose, but you may have a valid
> justification.]
>
> However, I don't know that drc handles replicate subjects (petri dishes)
> followed over time, where you need a random effect for subject.  [You don't
> say whether you have replicate soil samples followed over time.]  If you
> have replicate soil samples,  you could fit something like a generalized
> linear mixed model with lme4 or related, or generalized additive mixed
> model with mgcv or gamm4. family='binomial', and for each subject &
> species, the sum of the seeds that germinated as the total.
> Alternatively, there are a number of packages for survival or time to
> event analysis.  Your T50 is equivalent to the median survival time (or
> median time to germination).  Look at the survival analysis task view:
> *https://cran.r-project.org/web/views/Survival.html
> <https://cran.r-project.org/web/views/Survival.html>*
> You may be able to use the survival package, as median survival times are
> available in most packages.  Gordon Fox (currently at USF) wrote a book
> chapter on applying such methods to germination times (albeit using SAS not
> R at the time), and might be willing to send you a pdf.
> I hope that this helps you with your analyses.
>
> Tom 2
>
>
> On Thu, Jul 23, 2015 at 2:03 PM, Mehdi Abedi <abedimail at gmail.com> wrote:
>
>> Dear Colleagues,
>>
>> I am interested to calculate time to 50 percentage for count data.
>> I am working on soil seed bank germination. I have recorded number of
>> seedling emergence in 10 different times for species. The total number of
>> seeds in soil is not known therefore it is not proportional data but we
>> can
>> argue that after this period all viable seeds already germinated(total
>> seedling emergence).
>>
>> I am familiar with drc package for calculation T50 but only for
>> proportional data like germination in petridishes which total number of
>> seed in each pteridishes is known  T50 could be calculated.
>>
>> Could we calculate T50 for count data as well? because we have total
>> seedling emergence in the end, therefore their distribution during time is
>> important and having this index we can find when species germinate ...
>> This indices could be useful for other count data specially survival
>> studies.
>>
>> warm regards
>> Mehdi
>>
>>
>> *Mehdi Abedi Department of Range Management*
>>
>> *Faculty of Natural Resources & Marine Sciences *
>>
>> *Tarbiat Modares University (TMU) *
>>
>> *46417-76489, Noor*
>>
>> *Mazandaran, IRAN *
>>
>> *mehdi.abedi at modares.ac.ir <Mehdi.abedi at modares.ac.ir>*
>>
>> *Homepage
>> <http://www.modares.ac.ir/en/Schools/nat/Academic_Staff/~mehdi.abedi>*
>>
>> *Tel: +98-122-6253101 *
>>
>> *Fax: +98-122-6253499*
>>
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>>
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>
>
>
> --
> "Data is not information. Information is not knowledge. And knowledge is
> certainly not wisdom."
>    -- Clifford Stoll
>
> "Science is what we understand well enough to explain to a computer. Art
> is everything else we do."
>    -- Donald Knuth
>
> "If you find that you're spending almost all your time on theory, start
> turning some attention to practical things; it will improve your theories.
> If you find that you're spending almost all your time on practice, start
> turning some attention to theoretical things; it will improve your
> practice."
>   -- Donald Knuth
>
>


-- 


*Mehdi Abedi Department of Range Management*

*Faculty of Natural Resources & Marine Sciences *

*Tarbiat Modares University (TMU) *

*46417-76489, Noor*

*Mazandaran, IRAN *

*mehdi.abedi at modares.ac.ir <Mehdi.abedi at modares.ac.ir>*

*Homepage
<http://www.modares.ac.ir/en/Schools/nat/Academic_Staff/~mehdi.abedi>*

*Tel: +98-122-6253101 *

*Fax: +98-122-6253499*

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