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 find means of a factor that are significantly 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 significantly different one each other are represented with the same letter.

synonymous: Tukey’s range test / Tukey method / Tukey’s honest significance test / Tukey’s HSD (honest significant difference) test / Tukey–Kramer method

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# library library(multcompView) # Create data treatment=c(rep("A", 20) , rep("B", 20) , rep("C", 20), rep("D", 20) , rep("E", 20)) value=c( sample(2:5, 20 , replace=T) , sample(6:10, 20 , replace=T), sample(1:7, 20 , replace=T), sample(3:10, 20 , replace=T) , sample(10:20, 20 , replace=T) ) data=data.frame(treatment,value) # What is the effect of the treatment on the value ? model=lm( data$value ~ data$treatment ) ANOVA=aov(model) # Tukey test to study each pair of treatment : TUKEY <- TukeyHSD(x=ANOVA, 'data$treatment', conf.level=0.95) # Tuckey test representation : plot(TUKEY , las=1 , col="brown" ) # I need to group the treatments that are not different each other together. generate_label_df <- function(TUKEY, variable){ # Extract labels and factor levels from Tukey post-hoc Tukey.levels <- TUKEY[[variable]][,4] Tukey.labels <- data.frame(multcompLetters(Tukey.levels)['Letters']) #I need to put the labels in the same order as in the boxplot : Tukey.labels$treatment=rownames(Tukey.labels) Tukey.labels=Tukey.labels[order(Tukey.labels$treatment) , ] return(Tukey.labels) } # Apply the function on my dataset LABELS=generate_label_df(TUKEY , "data$treatment") # A panel of colors to draw each group with the same color : my_colors=c( rgb(143,199,74,maxColorValue = 255),rgb(242,104,34,maxColorValue = 255), rgb(111,145,202,maxColorValue = 255),rgb(254,188,18,maxColorValue = 255) , rgb(74,132,54,maxColorValue = 255),rgb(236,33,39,maxColorValue = 255),rgb(165,103,40,maxColorValue = 255)) # Draw the basic boxplot a=boxplot(data$value ~ data$treatment , ylim=c(min(data$value) , 1.1*max(data$value)) , col=my_colors[as.numeric(LABELS[,1])] , ylab="value" , main="") # I want to write the letter over each box. Over is how high I want to write it. over=0.1*max( a$stats[nrow(a$stats),] ) #Add the labels text( c(1:nlevels(data$treatment)) , a$stats[nrow(a$stats),]+over , LABELS[,1] , col=my_colors[as.numeric(LABELS[,1])] ) |

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`[mediatagger]`

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

Thanks in advance,

Q

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

Hey, thanks for this R-Script. It worked. But is it possible to modify this script to get graph and significant 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!!

I am a new R user. I want to perform Tukey’s Test on my data and generate plots,

so I tried loading my own data but when I run the “labels” I get an error:

Error in tukey[[variable]] : invalid subscript type ‘symbol’

Maybe your problema was caused by the square brackets… try using tukey$variable istead of tukey[[variable]]…

I am a new R user. I want to perform Tukey’s Test on my data and generate plots.

So I tried loading my own data but when I run the “labels” I get an error:

Error in tukey[[variable]] : invalid subscript type ‘symbol’

Please help!