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

[Manuel Esteban Lucas Borja]

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

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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/