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

[Philippi, Tom]

Mehdi--
You _can_ calculate estimates of the parameters at median germination from
the lme or gamm objects, but the confidence intervals are not easy.
I recommend using the survival package, specifically survfit.formula and
quantile.survfit, which gives a couple of examples

fit <- survfit(Surv(time, status) ~ ph.ecog, data=lung)

quantile(fit)

Tom 2

On Fri, Jul 24, 2015 at 12:43 AM, Mehdi Abedi <abedimail at gmail.com> wrote:

> 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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>>>
>>> _______________________________________________
>>> R-sig-ecology mailing list
>>> R-sig-ecology at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>>
>>
>>
>>
>> --
>> "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*
>



-- 
"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

-------------------------------------------
Tom Philippi, Ph.D.
Quantitative Ecologist & Data Therapist
Inventory and Monitoring Program
National Park Service
(619) 557-5450 x4576
Tom_Philippi at nps.gov
http://science.nature.nps.gov/im/monitor

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