Steffen Katzner
2006-Jan-18 12:12 UTC
[R] Within-Subjects ANOVA & comparisons of individual means
I am having problems with comparing individual means in a
within-subjects ANOVA. From my understanding, TukeyHSD is not
appropriate in this context. So I am trying to compute contrasts, as
follows:
seven subjects participated in each of 6 conditions (intervals).
> subject = factor(rep(c(1:7), each = 6))
> interval = factor(rep(c(1:6), 7))
and here is the dependent variable:
> dv = c(3.3868, 3.1068, 1.7261, 1.5415, 1.7356, 0.7538,
+ 2.5957, 1.5666, 1.1984, 1.2761, 1.0022, 0.8597,
+ 3.9819, 3.1506, 1.5824, 1.7400, 1.4248, 0.6519,
+ 2.2521, 1.5248, 1.1209, 1.2193, 1.1994, 2.0910,
+ 2.4661, 1.3863, 1.3591, 0.9163, 1.3976, 1.7471,
+ 3.2486, 1.9492, 2.4228, 1.1276, 1.2836, 0.9814,
+ 1.7148, 1.7278, 2.7433, 1.4924, 1.0992, 0.7821)
> d = data.frame(subject, interval, dv)
next I'm defining a contrast matrix:
> con = matrix(c(1, -1, 0, 0, 0, 0, 0, 1, -1, 0, 0, 0, 0, 0, 1, -1, 0,
0, 0, 0, 0, 1, -1, 0, 0, 0, 0, 0, 1, -1), nrow=6, ncol=5, byrow=F)
> con
[,1] [,2] [,3] [,4] [,5]
[1,] 1 0 0 0 0
[2,] -1 1 0 0 0
[3,] 0 -1 1 0 0
[4,] 0 0 -1 1 0
[5,] 0 0 0 -1 1
[6,] 0 0 0 0 -1
> contrasts(d$interval)=con
and then I'm doing the ANOVA
> aovRes = aov(dv~interval+Error(subject/interval), data=d)
> summary(aovRes)
Error: subject
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 6 2.48531 0.41422
Error: subject:interval
Df Sum Sq Mean Sq F value Pr(>F)
interval 5 13.8174 2.7635 8.7178 3.417e-05 ***
Residuals 30 9.5098 0.3170
---
Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1
but if I want to look at the contrasts, something has gone wrong:
summary.aov(aovRes, split=list(interval = list("i1 vs i2" = 1,
"i2 vs
i3" = 2, "i3 vs i4" = 3, "i4 vs i5" = 4, "i5 vs
i6" = 5)))
Error in 1:object$rank : NA/NaN argument
> aovRes$contrasts
NULL
Can anybody help?
Thank you very much, -Steffen
Steffen Katzner
2006-Jan-20 08:04 UTC
[R] Within-Subjects ANOVA & comparisons of individual means
I am having problems with comparing individual means in a within-subjects ANOVA. From my understanding, TukeyHSD is not appropriate in this context. So I am trying to compute contrasts, as follows: seven subjects participated in each of 6 conditions (intervals).> subject = factor(rep(c(1:7), each = 6)) > interval = factor(rep(c(1:6), 7))and here is the dependent variable:> dv = c(3.3868, 3.1068, 1.7261, 1.5415, 1.7356, 0.7538,+ 2.5957, 1.5666, 1.1984, 1.2761, 1.0022, 0.8597, + 3.9819, 3.1506, 1.5824, 1.7400, 1.4248, 0.6519, + 2.2521, 1.5248, 1.1209, 1.2193, 1.1994, 2.0910, + 2.4661, 1.3863, 1.3591, 0.9163, 1.3976, 1.7471, + 3.2486, 1.9492, 2.4228, 1.1276, 1.2836, 0.9814, + 1.7148, 1.7278, 2.7433, 1.4924, 1.0992, 0.7821)> d = data.frame(subject, interval, dv)next I'm defining a contrast matrix:> con = matrix(c(1, -1, 0, 0, 0, 0, 0, 1, -1, 0, 0, 0, 0, 0, 1, -1, 0,0, 0, 0, 0, 1, -1, 0, 0, 0, 0, 0, 1, -1), nrow=6, ncol=5, byrow=F)> con[,1] [,2] [,3] [,4] [,5] [1,] 1 0 0 0 0 [2,] -1 1 0 0 0 [3,] 0 -1 1 0 0 [4,] 0 0 -1 1 0 [5,] 0 0 0 -1 1 [6,] 0 0 0 0 -1> contrasts(d$interval)=conand then I'm doing the ANOVA> aovRes = aov(dv~interval+Error(subject/interval), data=d)> summary(aovRes)Error: subject Df Sum Sq Mean Sq F value Pr(>F) Residuals 6 2.48531 0.41422 Error: subject:interval Df Sum Sq Mean Sq F value Pr(>F) interval 5 13.8174 2.7635 8.7178 3.417e-05 *** Residuals 30 9.5098 0.3170 --- Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 but if I want to look at the contrasts, something has gone wrong: summary.aov(aovRes, split=list(interval = list("i1 vs i2" = 1, "i2 vs i3" = 2, "i3 vs i4" = 3, "i4 vs i5" = 4, "i5 vs i6" = 5))) Error in 1:object$rank : NA/NaN argument> aovRes$contrastsNULL Can anybody help? Thank you very much, -Steffen