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2008 Feb 25
0
Extracting variance components from a Manova
...e using estimates of the variance components based on the sums of squares from summary.manova()$SS is leading to an unacceptably large bias. It is clear we need to use a better method (ReML?) to estimate the covariance matrices! The code we use for running the manova: Y <- cbind(Pupal_Mass, Dev_Time, Dry_Weight, Rel_Fitness) sire <- factor(Sire) dam<- factor(Dam) fit <- manova(Y ~ sire + dam:sire) sireSS <- summary(fit)$SS$sire etc. the sire covariance matrix = (MS(sires) ? MS(dams)/(offspring/sire) which gives us the correct answer with balanced data, but of course not with unb...