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

[Thierry Onkelinx]

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/
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