Re: [R] Two-factor ANOVA Help

From: Gabor Grothendieck <ggrothendieck_at_gmail.com>
Date: Sun 09 Oct 2005 - 00:15:13 EST

On 10/8/05, Jim Brindle <j_brindle@hotmail.com> wrote:
> Hello,
>
> I am trying to perform a two-factor ANOVA analysis using a blocking design with "Vol" as the response variable. My intent is to have "Rater" treated as the treatment variable and the "Pipe" treated as the blocking variable. I am reading and preparing my dataset using the following three lines of code:
>
> values <- read.table("filename", header=TRUE)
> attach(values)
> values = data.frame(values)
>
> The dataset is the following:
>
> Pipe Rater Volume
> 1 A 5.129
> 1 B 5.296
> 1 C 4.679
> 1 D 4.776
> 2 A 8.519
> 2 B 8.482
> 2 C 7.659
> 2 D 7.798
> 3 A 13.769
> 3 B 14.621
> 3 C 12.418
> 3 D 13.189
>
> Below there are 2 versions which I've used to run my analysis.
>
> Option #1:
>
> g <- lm(Volume ~ factor(Rater) + factor(Pipe), values)
> print(anova(g))
>
> Option #2:
>
> Rater <- as.factor(Rater)
> Pipe <- as.factor(Pipe)
> g <- lm(Volume ~ Rater + Pipe, values)
> print(anova(g))
>
>
> A couple of questions I have are:
>
> 1. I thought that option #1 and option #2 would have given me the same results and they don't appear to. The only difference (to me) is how I have specified the factors used in the model. However, there appears to be something else I am missing and I was just wondering if anyone has any insight as to which is the correct way to code this analysis?

Note that values, as returned from read.table, is already a data frame and Rater is already a factor so you only need to convert Pipe to a factor:

values <- read.table("filename.dat", header = TRUE)

# shows classes of columns among other things # note that Rater is already a factor and values is already a data frame str(g)

# convert Pipe to a factor
values$Pipe <- factor(values$Pipe)
g <- lm(Volume ~., values)
g

>
> 2. Unless otherwise specified is there a particular reference level that R uses by default - for example in this case, the second treatment level (Rater B)?

By default R uses treatment contrasts and uses the first level as the baseline. You can change this using contrasts and contr.treatment.

 e.g. To use treatment effects on Pipe with level 2 as the baseline:

contrasts(values$Pipe) <- contr.treatment(3, base = 2) g2 <- lm(Volume ~., values)
g2

>
> 3. Is there a good reference someone can point me to for more insight on the two-factor ANOVA analysis with R?
>

See ?read.table, ?contrasts, ?contr.treatment



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