-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Ubuntu Diego
Sent: April-12-11 5:10 PM
To: r-help at r-project.org
Subject: [R] is this an ANOVA ?
Hi all,
I have a very easy questions (I hope). I had measure a property of plants, growing in three
different substrates (A, B and C). The rest of the conditions remained constant. There was very high
variation on the results.
I want to do address, whether there is any difference in the response (my measurement) from
substrate to substrate?
x<-c('A','A','A','A','A','B','B','B','B','B','C','C','C','C','C') # Substrate type
y <- c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15) # Results of the measurement
MD<-data.frame(x,y)
I wrote a linear model for this:
summary(lm(y~x,data=MD))
This is the output:
Call:
lm(formula = y ~ x, data = MD)
Residuals:
Min 1Q Median 3Q Max
-2.000e+00 -1.000e+00 5.551e-17 1.000e+00 2.000e+00
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 3.0000 0.7071 4.243 0.001142 **
xB 5.0000 1.0000 5.000 0.000309 ***
xC 10.0000 1.0000 10.000 3.58e-07 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 1.581 on 12 degrees of freedom
Multiple R-squared: 0.8929, Adjusted R-squared: 0.875
F-statistic: 50 on 2 and 12 DF, p-value: 1.513e-06
I conclude that there is an effect of substrate type (x).
NOW the questions :
1) Do the fact that the all p-values are significant means that all the groups are
different from each other ?
No, the small p-values indicate that the associated estimate appears to be significantly different from zero.
You can use the package "multcomp" to do multiple comparisons.
> require("multcomp")
> lma <- aov(y ~ x, data = MD)
> lmamc <- glht(lma, linfct = mcp(x = "Tukey"))
> ci.lma <- confint(lmamc)
> ci.lma
Simultaneous Confidence Intervals
Multiple Comparisons of Means: Tukey Contrasts
Fit: aov(formula = y ~ x, data = MD)
Quantile = 2.667
95% family-wise confidence level
Linear Hypotheses:
Estimate lwr upr
B - A == 0 5.0000 2.3330 7.6670
C - A == 0 10.0000 7.3330 12.6670
C - B == 0 5.0000 2.3330 7.6670
> lmacld <- cld(lmamc)
> plot(lmacld)
> plot(ci.lma)
2) Is there a (easy) way to plot, mean plus/minus 2*sd for each substrate type ? (with asterisks denoting significant differences ?)
Not that I know of, though the multcomp tables and plots yield logically equivalent results and plots. Writing a few lines of code to accomplish your graph is fairly straightforward. HTH Steven McKinney
THANKS ! version platform x86_64-apple-darwin9.8.0 arch x86_64 os darwin9.8.0 system x86_64, darwin9.8.0 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31)
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