Dear R users,

I am doing custom contrasts with R (comparison of group means).
Everything works fine, but I would like to test the 3 contrasts with and 
without a Welch correction for unequal variances.

I can replicate SPSS results when equal variances are assumed, but I do 
not manage to test the contrasts when equal variances are not assumed. I 
pasted below the results with R and SPSS (at the bottom of my email). R 
provides F, while SPSS provides t (F = t squared).

Is there a way to apply the Welch correction to custom contrasts with R 
anova function (or another correction for unequal variances, like 
Brown-Forsythe), or do I need to use another package when equal 
variances cannot be assumed ?

Regards,

Michael


==========================================
# R Syntax
==========================================

# c1 : group 1 vs. group 2.
# c2 : group 3 vs. group 4.
# c3 : group 1+2 vs. group 3+4.

c1 <- c(1, -1,  0,  0)
c2 <- c(0,  0,  1, -1)
c3 <- c(1,  1, -1, -1)

modele.global     <- lm(var ~ cond,
                      data=Plan_CR_4_Modifie)

modele.contrastes <- lm(var ~ C(cond, c1, 1)
                             + C(cond, c2, 1)
                             + C(cond, c3, 1),
                      data=Plan_CR_4_Modifie)

anova(modele.global)
anova(modele.contrastes)

------------------------------------------
R Results:

 > anova(modele.global)
Analysis of Variance Table

Response: var
           Df Sum Sq Mean Sq F value    Pr(>F)
cond       3     49 16.3333  7.4973 0.0007824 ***
Residuals 28     61  2.1786
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

 > anova(modele.contrastes)
Analysis of Variance Table

Response: var
                Df Sum Sq Mean Sq F value    Pr(>F)
C(cond, c1, 1)  1      1   1.000  0.4590 0.5036442
C(cond, c2, 1)  1     16  16.000  7.3443 0.0113548 *
C(cond, c3, 1)  1     32  32.000 14.6885 0.0006571 ***
Residuals      28     61   2.179
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1




==========================================
* SPSS Syntax - CONTRAST TESTS.
==========================================

ONEWAY
   var BY cond
   /CONTRAST= 1 -1 0 0  /CONTRAST= 0 0 1 -1  /CONTRAST= 1 1 -1 -1
   /STATISTICS DESCRIPTIVES HOMOGENEITY
   /MISSING ANALYSIS
   /POSTHOC = SCHEFFE LSD BONFERRONI ALPHA(.05).


------------------------------------------
SPSS Results - Contrasts:

Assume equal variances

|--------|-----------------|----------|------|------|---------------|
|Contrast|Value of Contrast|Std. Error|t     |df    |Sig. (2-tailed)|
|--------|-----------------|----------|------|------|---------------|
|1       |-.50             |.738      |-.678 |28 |.504           |
|--------|-----------------|----------|------|------|---------------|
|2       |-2.00            |.738      |-2.710|28 |.011           |
|--------|-----------------|----------|------|------|---------------|
|3       |-4.00            |1.044     |-3.833|28 |.001           |
--------------------------------------------------------------------|

Does not assume equal variances

|--------|-----------------|----------|------|------|---------------|
|Contrast|Value of Contrast|Std. Error|t     |df    |Sig. (2-tailed)|
|--------|-----------------|----------|------|------|---------------|
|1       |-.50             |.627      |-.798 |11.603|.441           |
|--------|-----------------|----------|------|------|---------------|
|2       |-2.00            |.835 |-2.397|10.155|.037           |
|--------|-----------------|----------|------|------|---------------|
|3       |-4.00            |1.044 |-3.833|19.431|.001           |
--------------------------------------------------------------------|


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