[R] Finding Interaction and main effects contrasts for two-wayANOVA

[Gregory Warnes]

Dale,

You might find it fruitful to look at the help pages for fit.contrast 
() and estimble() functions in the gmodels package, and the contrast 
() functions in the Hmisc package.

-Greg



On Mar 7, 2008, at 4:20PM , Thompson, David ((MNR)) wrote:

>  Dale,
>
> Other than the first SAS contrast, does the following demonstrate what
> your asking for?
>> summary(twoway)
>  material temp       voltage
>  1:12     50:12   Min.   : 20
>  2:12     65:12   1st Qu.: 70
>  3:12     80:12   Median :108
>                   Mean   :106
>                   3rd Qu.:142
>                   Max.   :188
>> contrasts(twoway$material)
>   2 3
> 1 0 0
> 2 1 0
> 3 0 1
>> contrasts(twoway$temp)
>    65 80
> 50  0  0
> 65  1  0
> 80  0  1
>> fit <- aov(voltage ~ material*temp, data=twoway)
>> summary.aov(fit)
>               Df Sum Sq Mean Sq F value  Pr(>F)
> material       2  10684    5342    7.91  0.0020 **
> temp           2  39119   19559   28.97 1.9e-07 ***
> material:temp  4   9614    2403    3.56  0.0186 *
> Residuals     27  18231     675
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
>
>
> # setting (partial) contrasts
>> contrasts(twoway$material) <- c(1,-1,0) # ignoring the second
> available df
>> contrasts(twoway$temp) <- c(0,1,-1) # ignoring the second  
>> available df
>> contrasts(twoway$material)
>   [,1]  [,2]
> 1    1 -0.41
> 2   -1 -0.41
> 3    0  0.82
>> contrasts(twoway$temp)
>    [,1]  [,2]
> 50    0 -0.82
> 65    1  0.41
> 80   -1  0.41
>
>> summary.aov(fit, split=list(material=list('m1-m2'=1), temp=list 
>> ('t50 -
> t80'=1)))
>                                  Df Sum Sq Mean Sq F value  Pr(>F)
> material                          2  10684    5342    7.91 0.00198 **
>   material: m1-m2                 1   3800    3800    5.63 0.02506 *
> temp                              2  39119   19559   28.97 1.9e-07 ***
>   temp: t50 - t80                 1  11310   11310   16.75 0.00035 ***
> material:temp                     4   9614    2403    3.56 0.01861 *
>   material:temp: m1-m2.t50 - t80  1   4970    4970    7.36 0.01146 *
> Residuals                        27  18231     675
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
>
> # other examples of setting contrasts
> # compare m1 vs m2 and m2 vs m3
>> contrasts(twoway$material) <- matrix(c(1,-1,0,1,1,-2), nrow=3)
>> contrasts(twoway$material)
>   [,1] [,2]
> 1    1    0
> 2   -1    1
> 3    0   -1
> # compare m1 vs m2 and m1+m2 vs m3
>> contrasts(twoway$material) <- matrix(c(1,-1,0,1,1,-2), nrow=3)
>> contrasts(twoway$material)
>   [,1] [,2]
> 1    1    1
> 2   -1    1
> 3    0   -2
>
> I'm not sure if 'summary.aov' is the only lm-family summary method  
> with
> the split argument.
>
> DaveT.
> *************************************
> Silviculture Data Analyst
> Ontario Forest Research Institute
> Ontario Ministry of Natural Resources
> david.john.thompson at ontario.ca
> http://ofri.mnr.gov.on.ca
> *************************************
>> -----Original Message-----
>> From: Steele [mailto:dale.w.steele at gmail.com]
>> Sent: March 6, 2008 09:08 PM
>> To: r-help at stat.math.ethz.ch
>> Subject: [R] Finding Interaction and main effects contrasts
>> for two-way ANOVA
>>
>> I've tried  without success to calculate interaction and main effects
>> contrasts using R.  I've found the functions C(), contrasts(),
>> se.contrasts() and fit.contrasts() in package gmodels.  Given the url
>> for a small dataset and the two-way anova model below, I'd like to
>> reproduce the results from appended SAS code.  Thanks.  --Dale.
>>
>>  ## the dataset (from Montgomery)
>> twoway <- read.table("http://dsteele.veryspeedy.net/sta501/ 
>> twoway.txt",
>> col.names=c('material', 'temp','voltage'),colClasses=c('factor',
>> 'factor', 'numeric'))
>>
>>  ## the model
>> fit <- aov(voltage ~ material*temp, data=twoway)
>>
>> /* SAS code */
>> proc glm data=twoway;
>> class material temp;
>> model voltage = material temp material*temp;
>> contrast '21-22-31+32' material*temp 0 0 0 1 -1 0 -1 1 0;
>> estimate '21-22-31+32' material*temp 0 0 0 1 -1 0 -1 1 0;
>> contrast 'material1-material2' material 1 -1 0;
>> estimate 'material1-material2' material 1 -1 0;
>> contrast 'temp50 - temp80' temp 1 0 -1;
>> estimate 'temp50 - temp80' temp 1 0 -1;
>> run;
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting- 
> guide.html
> and provide commented, minimal, self-contained, reproducible code.