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

[Philippi, Tom]

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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