Two way repeated measures analysis in R

-

In this tutorial you will learn how to carry out analysis for two way repeated measures anova using R studio. A two way repeated measures anova compares the mean differences between groups that have been split on two within subject factors. These factors are also known as independent variables.

Two way repeated measures anova is also known as:

  • Two factor repeated measures anova
  • Two factor or two way anova with repeated measures
  • Within within subjects anova

A two way repeated measures anova is often used in studies where you have measured:

  • A dependent variable over two or more time points
  • When subjects have undergone two or more conditions

You should also know how to identify a two way repeated measures anova from mixed anova. Mixed anova is very similar to two way repeated measures anova because both tests involve two factors. In a mixed anova, subjects that undergo each condition are different. Whereas in two way repeated measures anova same subjects undergo both conditions.

Description of data

The data file which is used for analysis contains subject ID, condition, time interval and response variable. Here subject ID represents the subjects or individuals used to record the response variable measurements. These subjects have a condition where male and female individuals were used. The response variable measurements were recorded at a four different time intervals. In this data set you can see the same subjects were repeated to record the response variable at different time intervals rather than using different individuals. As same subjects were repeated, so we shall proceed with two way repeated measures anova in R studio.

Clear R environment

As a first step, I always recommend to clear data objects and values in global environment with rm() function. Set TRUE value for the argument all to remove objects and values if you have created earlier. Shut down all the graphic windows by using graphics.off() function. Putting the value “cls” in shell() function will clear the console environment.

rm(list = ls(all = TRUE))
graphics.off()
shell("cls")

Importing data

To import the data set I have placed the CSV data file in the project working directory. Create an object data and assign to it a function which I am calling as read.csv(). In argument file after equal sign within quotations just press tab button to access the files present in the working directory. Now we need to choose the respective CSV data file. In the next argument header type TRUE to indicate that the first row of the data file contains variable names or headings.

In the next line we can use the head() function to print the first six rows of the data frame. Here I am converting the first 2 variables as factor variables by using as.factor() function. Use attach() function for data object to mask the components of the variables in the data frame.

data <- read.csv(file = "data.csv", 
                 header = TRUE)
head(data)

data$group = as.factor(data$group)
data$time = as.factor(data$time)
attach(data)
#   subID  group time resp.var
# 1     1   male day1       26
# 2     2   male day1       27
# 3     3   male day1       24
# 4     4 female day1       18
# 5     5 female day1       17
# 6     6 female day1       16

Fitting ANOVA model

Let’s proceed with analysis of variance to see how the response variable changes as the function of condition and time applied to each participant. The aov() function is used to fit analysis of variance model. The function is same as used in two way anova with only difference in error argument. Here you need to define error as ratio between subject ID and interaction of group and time factor. For denominator you can also use group, time and interaction term combined with plus sign. Summary() function for model object will print the results.

model.aov <- aov(resp.var ~ 
                           group * time + 
                           Error(subID/(group*time)))
#OR
model.aov <- aov(resp.var ~
                           group * time + 
                           Error(subID/(group + time + group:time)))

summary(model.aov)
# 
# Error: subID
#       Df Sum Sq Mean Sq
# group  1    408     408
# 
# Error: subID:group
#       Df Sum Sq Mean Sq
# group  1  67.25   67.25
# 
# Error: subID:time
#      Df Sum Sq Mean Sq
# time  3  356.7   118.9
# 
# Error: subID:group:time
#      Df Sum Sq Mean Sq
# time  3  49.94   16.65
# 
# Error: Within
#            Df Sum Sq Mean Sq F value  Pr(>F)   
# group       1  13.86  13.863   6.105 0.03866 * 
# time        3  52.79  17.596   7.749 0.00943 **
# group:time  3   2.60   0.868   0.382 0.76887   
# Residuals   8  18.17   2.271                   
# ---
# Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

The results showed that the error function has decomposed the residuals into:

  • Subject ID
  • Subject ID and group interaction
  • Subject ID and time interaction
  • Three way interaction of subject ID, group and time

This decomposition of error term considerably reduce the residual source of variance for the calculation of F value. Both the time and group variables significantly influence the response variable. However, their interaction was non-significant.

Mean comparison test

Now let’s compute mean comparisons to observe the differences between main effects.

SNK test

SNK test is derived from Tukey, but it is less conservative. Tukey test controls the error for all comparisons, where SNK only controls for comparisons under consideration. Before using SNK.test() function, first define error degree of freedom and error mean square value that will be used in this function.

Edf <- df.residual(model.aov$Within)
Edf
# [1] 8
EMS <- deviance(model.aov$Within)/Edf
EMS
# [1] 2.270833

To apply SNK test use SNK.test() function. This function requires:

  • Y argument that specify the response variable
  • TRT argument that represents the treatment factor variable applied to each experimental unit as group and time in this example.
  • DF error and MS error represents degree of freedom and mean square for error term as determined earlier
  • Alpha shows the significance level. Default value is 5 percent.
  • Group argument specify the formation of treatment groups. True value for group will result in treatment groups with lettering. False value for group will provide information regarding comparisons between treatments.
library(agricolae)
SNK.test1 <- SNK.test(y = resp.var,
                     trt = group,
                     DFerror = Edf,
                     MSerror = EMS,
                     alpha = 0.05,
                     group = TRUE)
print(SNK.test1)
# $statistics
#    MSerror Df     Mean       CV
#   2.270833  8 14.33333 10.51345
# 
# $parameters
#   test name.t ntr alpha
#    SNK  group   2  0.05
# 
# $snk
#      Table CriticalRange
# 2 3.261182      1.418656
# 
# $means
#         resp.var      std  r Min Max   Q25  Q50   Q75
# female  9.833333 4.687184 12   4  18  6.75  9.0 11.50
# male   18.833333 4.687184 12  13  27 15.75 17.5 21.75
# 
# $comparison
# NULL
# 
# $groups
#         resp.var groups
# male   18.833333      a
# female  9.833333      b
# 
# attr(,"class")
# [1] "group"

Similarly, for mean comparisons in time variable just replace group with time in trt argument.

SNK.test2 <- SNK.test(y = resp.var,
                     trt = time,
                     DFerror = Edf,
                     MSerror = EMS,
                     alpha = 0.05,
                     group = TRUE)
print(SNK.test2)
# $statistics
#    MSerror Df     Mean       CV
#   2.270833  8 14.33333 10.51345
# 
# $parameters
#   test name.t ntr alpha
#    SNK   time   4  0.05
# 
# $snk
#      Table CriticalRange
# 2 3.261182      2.006283
# 3 4.041036      2.486050
# 4 4.528810      2.786128
# 
# $means
#       resp.var      std r Min Max   Q25  Q50   Q75
# day1 21.333333 4.885352 6  16  27 17.25 21.0 25.50
# day2 13.833333 6.145459 6   7  21  9.00 13.5 18.75
# day3 12.500000 3.937004 6   8  17  9.25 12.5 15.75
# day4  9.666667 5.240865 6   4  16  5.25  9.5 13.75
# 
# $comparison
# NULL
# 
# $groups
#       resp.var groups
# day1 21.333333      a
# day2 13.833333      b
# day3 12.500000      b
# day4  9.666667      c
# 
# attr(,"class")
# [1] "group"

Visualizing results

Barplot for time variable

You can plot bar graph with standard error at the top of each bar from the output of SNK test applied earlier. The below code shows how the plot will be drawn using ggplot() function.

library(ggplot2)

SE1 = SNK.test1$means$std/sqrt(SNK.test1$means$r)

ggplot(data=SNK.test1$means, 
       aes(x= rownames(SNK.test1$means), 
           y= resp.var, 
           fill=rownames(SNK.test1$means))) +
  geom_bar(stat="identity") +
  geom_errorbar(aes(ymax = resp.var + std/sqrt(r),
                    ymin = resp.var - std/sqrt(r)), 
                position = position_dodge(width=0.9), 
                width = 0.25) +
  labs(title = "",
       x = "group",
       y = "Response variable",
       fill = "group") +
  geom_text(data = SNK.test1$groups, 
            aes(x = rownames(SNK.test1$groups),
                y = resp.var + SE1,
                label = as.matrix(groups)),
            position = position_dodge(width = 0.9),
            vjust = -(0.5))

Barplot for group variable

SE2 = SNK.test2$means$std/sqrt(SNK.test2$means$r)

ggplot(data=SNK.test2$means, 
       aes(x= rownames(SNK.test2$means), 
           y= resp.var, 
           fill=rownames(SNK.test2$means))) +
  geom_bar(stat="identity") +
  geom_errorbar(aes(ymax = resp.var + std/sqrt(r),
                    ymin = resp.var - std/sqrt(r)), 
                position = position_dodge(width=0.9), 
                width = 0.25) +
  labs(title = "",
       x = "time",
       y = "Response variable",
       fill = "time") +
  geom_text(data = SNK.test2$groups, 
            aes(x = rownames(SNK.test2$groups),
                y = resp.var + SE2,
                label = as.matrix(groups)),
            position = position_dodge(width = 0.9),
            vjust = -(0.5))

Please comment below if you have any questions.

Download data file — Click_here

Download Rscript — Click_here

Download R program — Click_here

Download R studio — Click_here

Comments

Post a Comment

Popular posts from this blog

Split plot analysis in R

-
Image
See Video   ⮞  ☝ AGRON Stats June 26, 2018 Description of design Import data file Observe variables Fit analysis of variance model Mean separation test Get error df and error MS values LSD test on main effects LSD test on interaction term Plot variation Plot bargraphs Main effects Interaction effect You will learn how to carry out split plot analysis, mean separation test using LSD.test() function and plotting the main and interaction effects using base graphics functions in R studio. Description of design Split-plot design is frequently used for factorial experiments. Such design may incorporate one or more of the completely randomized, completely randomized block, and Latin square designs. The main principle is that there are whole plots or whole units, to which the levels of one or more factors are applied. Thus each whole plot becomes a bloc
Read more

Elegant barplot using ggplot function in R

-
Image
See Video   ⮞  ☝ AGRON Stats August 03, 2020 In this post, you will learn how to import data, fit analysis of variance model, make comparison of treatments using LSD test and finally visualizing data by plotting bar graphs with standard error bars and placing alphabets from mean LSD test on top of error bars.  Introduction Importing data file Fit analysis of variance model LSD mean comparison test Original order of groups (for lettering) Visualizing effects Plotting genotypes Plotting gender Plotting interaction Introduction You will learn how to visualize bar graph for main and interaction effects using R studio. I shall use two way analysis of variance technique to fit a model for the given data set. Least significant difference test will be applied for mean comparisons. Bar graphs will be plotted using the alphabets from group component of LSD test to place just above the error
Read more