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*
T50 or ED50 for count data
4 messages · Mehdi Abedi, 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* [[alternative HTML version deleted]]
_______________________________________________ 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 [[alternative HTML version deleted]]
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* [[alternative HTML version deleted]]
_______________________________________________ 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* [[alternative HTML version deleted]]
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* [[alternative HTML version deleted]]
_______________________________________________ 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 [[alternative HTML version deleted]]