One-way ANOVA (cont.)

February 12, 2010
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(This article was first published on Software for Exploratory Data Analysis and Statistical Modelling, and kindly contributed to R-bloggers)

In a previous post we considered using R to fit one-way ANOVA models to data. In this post we consider a few additional ways that we can look at the analysis.

In the analysis we made use of the linear model function lm and the analysis could be conducted using the aov function. The code used to fit the model is very similar:

> plant.mod2 = aov(weight ~ group, data = plant.df)
> summary(plant.mod2)
            Df  Sum Sq Mean Sq F value  Pr(>F)  
group        2  3.7663  1.8832  4.8461 0.01591 *
Residuals   27 10.4921  0.3886                  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

The output from using the summary function of the fitted model object shows the analysis of variance table with the p-value showing evidence of differences between the three groups. In R we can investigated the particular groups where there are differences using Tukey’s multiple comparisons:

> TukeyHSD(plant.mod2)
  Tukey multiple comparisons of means
    95% family-wise confidence level
 
Fit: aov(formula = weight ~ group, data = plant.df)
 
$group
                          diff        lwr       upr     p adj
Treatment 1-Control     -0.371 -1.0622161 0.3202161 0.3908711
Treatment 2-Control      0.494 -0.1972161 1.1852161 0.1979960
Treatment 2-Treatment 1  0.865  0.1737839 1.5562161 0.0120064

The multiple comparison tests highlight that the difference is due to comparing treatments 1 and 2. These 95% confidence intervals for the differences shown above can be plotted:

plot(TukeyHSD(plant.mod2))

which gives

Tukey HSD Plot

The post-hoc adjustments are recommended as we are testing after looking at the data rather than undertaking a pre-planned analysis.

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