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I have a study design on two sites (each site was set up in a different way) and am trying to find the best approach for the analysis. I'm looking at survival of plant species, under 4 treatments, on 2 sites. Site 1 is blocked by treatment and site 2 is blocked by tree species. Before I realized the 2 sites were set up differently, I planned on running a nested ANOVA or a Mixed Model Regression but I'm confused on how to proceed as is. Coding (using R) in the block effect will just lead to co-linearity on Site 2 with my oaks, right? I suppose I could analyze the sites separately, but I want to know if there is a way to analyze them together. I uploaded a diagram of the study design. The study is balanced, there are 5 subplots/block. Appreciate any advice.

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    $\begingroup$ Go to the people who did this study and tell them "THIS is why you should consult the statistician EARLY!" $\endgroup$
    – Peter Flom
    Commented Jul 10 at 17:10
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    $\begingroup$ I did. They don't understand that the post-mortem for this kind of thing is difficult. I have made a check list that needs to be reviewed and answered for upcoming studies. $\endgroup$ Commented Jul 10 at 17:40

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Here's what I came up with for this issue: In this particular design my blocks were close to one another in proximity and running the above regression showed low level residuals by block. So I dropped block and added site as a fixed factor to incorporate the limitations of the design. Running this way puts some limits on being able to extrapolate the study to a broader whole but it gets around the initial issues. Simple fix, hopefully it's helpful to someone in a similar situation.

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