R 3.2.0

OS X

Colleagues,

I am confused about the implementation of contrasts in ANOVA. I have 4 groups (BATCH) in DATA. My code reads:

contrasts(DATA$BATCH) <- c(-1, -1, 1, 1)/2

LM <- lm(VALUES ~ SIDN + BATCH, data=DATA)

where both SIDN and BATCH are factors and VALUES is a real number

When I run this code, I get the exact results that a colleague obtains in SAS. So far, so good. Also, when I examine DATA$BATCH, i get:

> DATA$BATCH

[1] P R S Q R P S Q R P S Q P R Q S R P S Q R P Q S P R Q S P R Q S P R S Q P R

[39] S Q P R Q S R P Q S R P S Q R P Q S P R S Q R P Q S R P S Q R P Q S P R S Q

[77] P R S Q R P S Q P R Q S R P Q S P R Q S

attr(,"contrasts")

[,1] [,2] [,3]

P -0.5 -0.5 -0.5

Q -0.5 0.5 0.5

R 0.5 0.5 -0.5

S 0.5 -0.5 0.5

Levels: P Q R S

I noted that columns 2 and 3 did not seem relevant. Out of curiosity, I modified the contrasts code:

contrasts(DATA$BATCH, how.many=1) <- c(-1, -1, 1, 1)/2

Now when I examine DATA$BATCH, I get:

> DATA$BATCH

[1] P R S Q R P S Q R P S Q P R Q S R P S Q R P Q S P R Q S P R Q S P R S Q P R

[39] S Q P R Q S R P Q S R P S Q R P Q S P R S Q R P Q S R P S Q R P Q S P R S Q

[77] P R S Q R P S Q P R Q S R P Q S P R Q S

attr(,"contrasts")

[,1]

P -0.5

Q -0.5

R 0.5

S 0.5

Levels: P Q R S

This matches the previous output except for the disappearance of columns 2 and 3. I thought that would be desirable.

When I now run the code, the estimate for BATCH did not change — however, its SE (and the resulting t value) changed 10%.

I don’t understand how the

how.many

option in contrasts works. Can anyone offer an explanation?

Thanks in advance.

Dennis

Dennis Fisher MD

P < (The "P Less Than" Company)

Phone: 1-866-PLessThan (1-866-753-7784)

Fax: 1-866-PLessThan (1-866-753-7784)

www.PLessThan.com

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