7/2/2019 #84 Tukey test – The R Graph Gallery

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#84 TUKEY TEST

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Tukey’s test is a single-step multiple comparison procedure and statistical test. It is a post-hoc analysis,
what means that it is used in conjunction with an ANOVA. It allows to nd means of a factor that are
signi cantly different from each other, comparing all possible pairs of means with a t-test like method.
You can read this page if you want to understand the exact procedure of this test.

Results are usually drawn in a boxplot. Levels that are not signi cantly different one each other are
represented with the same letter.

synonymous: Tukey’s range test / Tukey method / Tukey’s honest signi cance test / Tukey’s HSD
(honest signi cant difference) test / Tukey–Kramer method

1 # library
2 library(multcompView)
3  
4 # Create data
5 treatment=c(rep("A", 20) , rep("B", 20) , rep("C", 20), rep("D", 20) ,  rep("E", 20))
6 value=c( sample(2:5, 20 , replace=T) , sample(6:10, 20 , replace=T), sample(1:7, 20 , re
7 data=data.frame(treatment,value)
8  
9 # What is the effect of the treatment on the value ?
10 model=lm( data$value ~ data$treatment )
11 ANOVA=aov(model)
12  
13 # Tukey test to study each pair of treatment :
14 TUKEY <- TukeyHSD(x=ANOVA, 'data$treatment', conf.level=0.95)
15  
16 # Tuckey test representation :
17 plot(TUKEY , las=1 , col="brown" )
18  
19  
20 # I need to group the treatments that are not different each other together.

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21 generate_label_df <- function(TUKEY, variable){
22  
23      # Extract labels and factor levels from Tukey post-hoc
24      Tukey.levels <- TUKEY[[variable]][,4]
25      Tukey.labels <- data.frame(multcompLetters(Tukey.levels)['Letters'])
26     
27      #I need to put the labels in the same order as in the boxplot :
28      Tukey.labels$treatment=rownames(Tukey.labels)
29      Tukey.labels=Tukey.labels[order(Tukey.labels$treatment) , ]
30      return(Tukey.labels)
31      }
32  
33 # Apply the function on my dataset
34 LABELS=generate_label_df(TUKEY , "data$treatment")
35  
36  
37 # A panel of colors to draw each group with the same color :
38 my_colors=c( rgb(143,199,74,maxColorValue = 255),rgb(242,104,34,maxColorValue = 255), rg
39  
40 # Draw the basic boxplot
41 a=boxplot(data$value ~ data$treatment , ylim=c(min(data$value) , 1.1*max(data$value)) ,
42  
43 # I want to write the letter over each box. Over is how high I want to write it.
44 over=0.1*max( a$stats[nrow(a$stats),] )
45  
46 #Add the labels
47 text( c(1:nlevels(data$treatment)) , a$stats[nrow(a$stats),]+over , LABELS[,1]  , col=my

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Eleftheria 

Many thanks for this! Do you know of a code for checking the assumptions fro the TukeyHSD test
Guest in R? Thanks again!

 0    Reply  2 months ago

Bien 

Many thanks. It is exactly what I need. Love from Vietnam

Guest
 0    Reply  4 months ago

Quin 

Hello, This is exactly the graph I’d like to build for my data.! Thanks so much for writing this. I am
Guest wondering, how would you order the levels from highest means to lowest?

Thanks in advance,
Q

 8    Reply  1 year ago 

Lochs 

You could probably achieve this by ordering your categorical factors in your data frame by
Guest
their mean values? Then just produce the plot as normal.

 1   Reply  2 months ago

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Diana 
what is the treatment and value???? im failing to interprete them. trying to use the
code on my data. thanx.
Guest

 0    Reply  2 years ago

Ayush Gyawali 

Hey, thanks for this R-Script. It worked. But is it possible to modify this script to get graph and
Guest signi cant letters in terms of a factorial design?
For example
In case of code- LABELS=generate_label_df(TUKEY , “x$Treatment”)
If Treatment and Depth are two Treatments in a factorial design then can this above be written
as..
code – LABELS=generate_label_df(TUKEY , “x$Treatment”, “x$Depth”)????
Thanks in advance!!

 0    Reply  2 years ago

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