[R-sig-eco] Natural regeneration experiment using R

Mon Mar 30 16:52:29 CEST 2015

Ok, perfect. 

- In relation to NDied, I have to calculate the number of died seedlings as a new column since the model you proposed uses the number of survived and died seedlings, true?
-  Do I have to use the same model to evaluate seed emergence?
- Are you agree that this is a nested experiment design? 

Thank you very much, 
---
Manuel Esteban Lucas Borja
Universidad de Castilla La Mancha
Escuela Técnica Superior de Ingenieros Agrónomos y de Montes 
Departamento de Ciencia y Tecnología Agroforestal y Genética
Campus Universitario s/n,
C.P. 02071, Albacete (Spain)
Télf.; 967599200 ext. 2818
Mail: ManuelEsteban.Lucas at uclm.es
Web:http://www.uclm.es/profesorado/manuelestebanlucas/

El 30/03/2015, a las 15:15, Thierry Onkelinx <thierry.onkelinx at inbo.be> escribió:

> Yes you need the number of seeds because the distribution is discrete. E.g. with 4 seeds only 0%, 25%, 50%, 75% or 100% can survive.
> 
> I notice a typo in my code. You need to specify the distribution as well. 
>> library(lme4)
>> model <- glmer(cbind(NSurvived, NDied) ~ Site * Condition * Protection + (1|Plot), data = your.dataset, family = binomial)
> 
> 
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest 
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance 
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> 
> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner 
> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
> 
> 2015-03-30 15:09 GMT+02:00 Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es>:
> Dear Thierry, 
> 
> Thank you so much. Please see in attachment the .txt file (sorry about the xls fiel).
> 
> Following your recommendation, I have to use the number of seeds and not the percentage, true?
> 
> Sincerely, 
> ---
> Manuel Esteban Lucas Borja
> Universidad de Castilla La Mancha
> Escuela Técnica Superior de Ingenieros Agrónomos y de Montes 
> Departamento de Ciencia y Tecnología Agroforestal y Genética
> Campus Universitario s/n,
> C.P. 02071, Albacete (Spain)
> Télf.; 967599200 ext. 2818
> Mail: ManuelEsteban.Lucas at uclm.es
> Web:http://www.uclm.es/profesorado/manuelestebanlucas/
> 
> 
> El 30/03/2015, a las 14:57, Thierry Onkelinx <thierry.onkelinx at inbo.be> escribió:
> 
>> Dear Manuel,
>> 
>> You can solves this with a mixed model. Something like 
>> 
>> library(lme4)
>> model <- glmer(cbind(NSurvived, NDied) ~ Site * Condition * Protection + (1|Plot), data = your.dataset)
>> 
>> Note that the list only allows several types of attachments. xls files are striped.
>> 
>> You might want to do some reading (e.g. Zuur et al, 2009) or consult a local statistician.
>> 
>> Best regards,
>> 
>> ir. Thierry Onkelinx
>> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest 
>> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance 
>> Kliniekstraat 25
>> 1070 Anderlecht
>> Belgium
>> 
>> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
>> The plural of anecdote is not data. ~ Roger Brinner 
>> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
>> 
>> 2015-03-30 14:31 GMT+02:00 Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es>:
>> Dear all,
>> 
>> I am just starting with R program and I would be very grateful if you could help me about how to analyze the data.  I am involved in a Pinus nigra regeneration experiment in Cuenca Mountains (Spain).  The aim of the study is to evaluate the effect of fire, soil preparation (scalping) and control (without treatment) on seed emergence and seedling survival in two sites (pure and mixed pinus nigra stands). Also seed predation effect will be evaluated using traps to protect the seeds and seedlings.
>> 
>> Different sowing points (subplots 25x25 cm) were sown using 6 pinus nigra seeds previously collected in the field. Variable response is seed emergence rate (%) and seedling survival rate (%) at the end of the experiment (1 year)
>> 
>> The experimental design is as follow:
>> 
>> - Three factors: Site, condition and seed protection.
>> 
>> - Levels of each factor:
>> 
>>             - Two sites (a mixed stand and a pure stand)
>> 
>>             - Three conditions (postfire, scalping and control)
>> 
>>             - Protection of seeds (yes or not)
>> 
>> Five plots were established at each condition and two subplots were established at each plot (A and B). Each subplot is considered as sowing points being one protected against predators and the other not.
>> 
>> 2 sites x 3 conditions x 2 seed protection x 5 plots x 2 sowing points= 120 (n=observations)
>> 
>> Please see attached .xls file to explore the data.
>> 
>> As far as I know, the experimental design can be considerer as nested since the factor “condition” is nested in the site factor (control level is not the same for mixed stand or pure stand). All the factors are fixed.
>> 
>> On these context my questions is how to analyze the data? And how to perform the analysis using the R program? I am thinking to use GML models but maybe using an ANOVA being condition factor nested in the site factor is easier.
>> 
>> Thank you so much. Any help is more than welcome.
>> 
>> Manuel
>> 
>> ---
>> Manuel Esteban Lucas Borja
>> Universidad de Castilla La Mancha
>> Escuela Técnica Superior de Ingenieros Agrónomos y de Montes
>> Departamento de Ciencia y Tecnología Agroforestal y Genética
>> Campus Universitario s/n,
>> C.P. 02071, Albacete (Spain)
>> Télf.; 967599200 ext. 2818
>> Mail: ManuelEsteban.Lucas at uclm.es
>> Web:http://www.uclm.es/profesorado/manuelestebanlucas/
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>> 
> 
> 
> 

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