output from multcomp and lm
Dear Hiroto, The anova() function reports a sequential analysis of variance, so the test for Cond ignores the covariate. A good guess is that the effect of Cond isn't significant controlling for the covariate. You could instead use drop1() or Anova() in the car package. I hope that this helps, John
At 10:46 AM 2/3/2004 +0900, Hiroto Miyoshi wrote:
Dear R-users I analysed the same data set by two different ways; analysis of covariance by using lm and anova functions and multiple comparison by using simtest function in the multcomp library. The output from the analysis of covariance is;
y<-lm(D~Cond+Q1,data=x) anova(y)
Analysis of Variance Table
Response: D
Df Sum Sq Mean Sq F value Pr(>F)
Cond 2 1017.8 508.9 4.7548 0.0135041 *
Q1 1 1652.7 1652.7 15.4417 0.0002969 ***
Residuals 44 4709.2 107.0
---
Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1
where Cond is a factor with three levels (A,B,C)
and Q1 is a covariate.
Now, simtest showed the following output
o5<-summary(simtest(D~Cond+Q1,conf.level=0.95,data=x,type="Tukey")) o5
Simultaneous tests: Tukey contrasts
Call:
simtest.formula(formula = D ~ Cond + Q1, data = x, conf.level = 0.95,
type = "Tukey")
Tukey contrasts for factor Cond, covariable: Q1
Contrast matrix:
CondA CondB CondC
CondB-CondA 0 -1 1 0 0
CondC-CondA 0 -1 0 1 0
CondC-CondB 0 0 -1 1 0
Absolute Error Tolerance: 0.001
Coefficients:
Estimate t value Std.Err. p raw p Bonf p adj
CondB-CondA 5.555 -1.461 3.802 0.151 0.453 0.319
CondC-CondB -5.248 -1.365 3.661 0.179 0.453 0.319
CondC-CondA 0.306 -0.084 3.844 0.934 0.934 0.934
The results from two analyses seem so different that I am
wondering why. I do understand that multiple comparison may
not show any significant difference even when the overall analysis
of (co)variance shows the statistical significance of a factor.
However, in my analysis, overall analysis showed statistical significance of
1.4% level and mutiple comparison showed significance of 32% level
Could this happen? and why? Please enlighten me.
] ----------------------------------------------------- John Fox Department of Sociology McMaster University Hamilton, Ontario, Canada L8S 4M4 email: jfox at mcmaster.ca phone: 905-525-9140x23604 web: www.socsci.mcmaster.ca/jfox