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

[Thierry Onkelinx]

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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