Clarification on ANOVA calculation without intercept in design in the vignette

[AliYoussef96]

Hi,

Thanks for the great package.

I had a quick question about this part of the ANOVA analysis section code in the vignette.

From my understanding, the code would produce valid results if the contrasts were defined using:

fit1 <- contrasts.fit(fit1, contrasts = contrast)

before calculating the ordinary t-statistic using:

ord.t = fit1$coefficients[, 1] / fit1$sigma / fit1$stdev.unscaled[, 1]

However, it appears that in the vignette, contrasts.fit was not used on fit1, and the code proceeds directly with fit1 without specifying contrasts. Could this produce incorrect results for the ANOVA?

Thank you!