Comparing Means of Two Groups in R

Sign Test in R

The sign test is used to compare the medians of paired or matched observations. It is an alternative to the paired-samples t-test (Chapter @ref(t-test)) and the Wilcoxon signed-rank test (Chapter @ref(wilcoxon-test)) in the situation, where the distribution of differences between paired data values is neither normal (in t-test) nor symmetrical (in Wilcoxon test).

Note that, the sign test does not make any assumptions about the data distributions. However, it will most likely be less powerful compared to the Wilcoxon test and the t-test.

Therefore, if the distribution of the differences between the two paired groups is symmetrical in shape, you could consider using the more powerful Wilcoxon signed-rank test instead of the sign test.

In this chapter, you will learn how to compute paired-samples sign test using the R function sign_test() [rstatix package].

Contents:

Related Book

Practical Statistics in R II - Comparing Groups: Numerical Variables

Prerequisites

Make sure that you have installed the following R packages:

  • tidyverse for data manipulation and visualization
  • ggpubr for creating easily publication ready plots
  • rstatix provides pipe-friendly R functions for easy statistical analyses
  • datarium: contains required datasets for this chapter

Start by loading the following required packages:

library(tidyverse)
library(rstatix)
library(ggpubr)

Demo dataset

Here, we’ll use a demo dataset mice2 [datarium package], which contains the weight of 10 mice before and after the treatment.

# Wide data
data("mice2", package = "datarium")
head(mice2, 3)
##   id before after
## 1  1    187   430
## 2  2    194   404
## 3  3    232   406
# Transform into long data: 
# gather the before and after values in the same column
mice2.long <- mice2 %>%
  gather(key = "group", value = "weight", before, after)
head(mice2.long, 3)
##   id  group weight
## 1  1 before    187
## 2  2 before    194
## 3  3 before    232

Statistical hypotheses

The paired-samples sign test evaluates whether the median of paired differences is statistically significantly different to 0.

  • Null hypotheses, H0: median of the paired differences = 0
  • Alternative hypotheses, Ha: median of the paired differences is different to 0

Summary statistics

Compute some summary statistics by groups: median and interquartile range (IQR).

mice2.long %>%
  group_by(group) %>%
  get_summary_stats(weight, type = "median_iqr")
## # A tibble: 2 x 5
##   group  variable     n median   iqr
##   <chr>  <chr>    <dbl>  <dbl> <dbl>
## 1 after  weight      10   405   28.3
## 2 before weight      10   197.  19.2

Visualization

bxp <- ggpaired(mice2.long, x = "group", y = "weight", 
         order = c("before", "after"),
         ylab = "Weight", xlab = "Groups")
bxp

Computation

Question : Is there any significant changes in the weights of mice after treatment?

stat.test <- mice2.long  %>%
  sign_test(weight ~ group) %>%
  add_significance()
stat.test
## # A tibble: 1 x 9
##   .y.    group1 group2    n1    n2 statistic    df       p p.signif
##   <chr>  <chr>  <chr>  <int> <int>     <dbl> <dbl>   <dbl> <chr>   
## 1 weight after  before    10    10        10    10 0.00195 **

Report

We could report the results as follow:

The median weight of the mice before treatment is significantly different from the median weight after treatment using sign test, p-value = 0.002.

stat.test <- stat.test %>% add_xy_position(x = "group")
bxp + 
  stat_pvalue_manual(stat.test, tip.length = 0) +
  labs(
  subtitle = get_test_label(stat.test, detailed= TRUE)
  )

Summary

This chapter describes how to compute and report the Sign test in R.

Wilcoxon Test in R (Prev Lesson)
Back to Comparing Means of Two Groups in R

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Alboukadel Kassambara
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