I have carried out an experiment that measured soil chemistry parameters at different times (0, 3, 6 and 9 months) from 12 plots in the field (3 treatments arranged in a fully randomized design with four replications). In each case, soil was randomly sampled in ten squares to give a composite soil sample per plot. Therefore, I believe that each soil is different. I statistically analysed with two-way ANOVA (with treatment and sampling date as factors). However, a colleague told me that since sampling dates are not independent from each other, it doesn’t make sense to use a two-way ANOVA with treatment and sampling date as orthogonal factors. Instead, a repeated measure ANOVA should be used. Which is correct?
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Repeated measures ANOVA is more appropriate. Your data are certainly correlated, since they are the same plots over time. Consider as well using a general linear mixed model or a covariance structure model as well, depending on whether the assumption of compound symmetry (used in RM-ANOVA) is valid. Good luck!
