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First herehere is my data. I had to link to it because of its size. Note that the biomass column has been standardized (mean = 0, sd = 1), hence the negative values. This does not alter the output. Once downloaded and the working directory has been specified, the file can be read in as follows:
First here is my data. I had to link to it because of its size. Note that the biomass column has been standardized (mean = 0, sd = 1), hence the negative values. This does not alter the output. Once downloaded and the working directory has been specified, the file can be read in as follows:
First here is my data. I had to link to it because of its size. Note that the biomass column has been standardized (mean = 0, sd = 1), hence the negative values. This does not alter the output. Once downloaded and the working directory has been specified, the file can be read in as follows:
These results clearly differ. The B:C interaction is no longer significant and the P-value for the A:B interaction is quite a bit higher. Both models should be computing the P-values in similar ways and so it's hard to imagine them being so different.
Why are they different?
###This was a part of the original question, but it can be misleading, see the answer below.
In fact, it seems that the anova(model, type = 3) function is actually using type 2 SS, which we can verify by running anova(model, type = 2).
The problem
These results clearly differ. The B:C interaction is no longer significant and the P-value for the A:B interaction is quite a bit higher. Both models should be computing the P-values in similar ways and so it's hard to imagine them being so different. In fact, it seems that the anova(model, type = 3) function is actually using type 2 SS, which we can verify by running anova(model, type = 2).
These results clearly differ. The B:C interaction is no longer significant and the P-value for the A:B interaction is quite a bit higher. Both models should be computing the P-values in similar ways and so it's hard to imagine them being so different.
Why are they different?
###This was a part of the original question, but it can be misleading, see the answer below.
In fact, it seems that the anova(model, type = 3) function is actually using type 2 SS, which we can verify by running anova(model, type = 2).
