TukeyHSD(model6, "as.factor(years)", ordered=FALSE)
  Tukey multiple comparisons of means
    95% family-wise confidence level

Fit: aov(formula = size_delta ~ as.factor(years) + site + size_start)

$`as.factor(years)`
                diff        lwr        upr p adj
1011-0910  1.3262044  1.1593278  1.4930810     0
1112-0910  0.6455031  0.4923524  0.7986538     0
1112-1011 -0.6807013 -0.8430464 -0.5183562     0

Warning message:
In replications(paste("~", xx), data = mf) :
  non-factors ignored: size_start

> TukeyHSD(model6, "site", ordered=FALSE)
  Tukey multiple comparisons of means
    95% family-wise confidence level

Fit: aov(formula = size_delta ~ as.factor(years) + site + size_start)

$site
          diff          lwr       upr     p adj
2-1  0.1699007 -0.007279693 0.3470812 0.0656746
3-1  0.1000283 -0.133933034 0.3339897 0.6891729
4-1  0.3486747  0.155559626 0.5417899 0.0000233
3-2 -0.0698724 -0.310180952 0.1704361 0.8772679
4-2  0.1787740 -0.021983872 0.3795319 0.1005857
4-3  0.2486464 -0.003640612 0.5009334 0.0551034

Warning message:
In replications(paste("~", xx), data = mf) :
  non-factors ignored: size_start