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

[Thierry Onkelinx]

- The model needs to know the number of both the alive and dead seedlings.
Hence you need two columns.
- Seed emergence can use a similar model.

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 16:52 GMT+02:00 Manuel Esteban Lucas Borja <
ManuelEsteban.Lucas at uclm.es>:

> 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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