An R Companion for the Handbook of Biological

Sta s cs
Salvatore S. Mangiafico

Student’s t–test for Two Samples

Introduction
When to use it
Null hypothesis
How the test works
Assumptions
See the Handbook for information on these topics.

Example
Two-sample t-test, independent (unpaired) observations
 
### --------------------------------------------------------------
### Two-sample t-test, biological data analysis class, pp. 128–129
### --------------------------------------------------------------
Input =("
Group Value
2pm    69   
2pm    70   
2pm    66   
2pm    63   
2pm    68   
2pm    70   
2pm    69   
2pm    67   
2pm    62   
2pm    63   
2pm    76   
2pm    59   
2pm    62   
2pm    62   
2pm    75   
2pm    62   
2pm    72    
2pm    63   
5pm    68
5pm    62
5pm    67
5pm    68
5pm    69
5pm    67
5pm    61
5pm    59
5pm    62
5pm    61
5pm    69
5pm    66
5pm    62
5pm    62
5pm    61
5pm    70
")
Data = read.table(textConnection(Input),header=TRUE)
bartlett.test(Value ~ Group, data=Data)
### If p-value >= 0.05, use var.equal=TRUE below
 
Bartlett's K-squared = 1.2465, df = 1, p-value = 0.2642
 
  
t.test(Value ~ Group, data=Data,
       var.equal=TRUE,
       conf.level=0.95)
 
Two Sample t-test
 
t = 1.2888, df = 32, p-value = 0.2067
 
 
t.test(Value ~ Group, data=Data,
       var.equal=FALSE,
       conf.level=0.95)
 
Welch Two Sample t-test
 
t = 1.3109, df = 31.175, p-value = 0.1995
 
 
Plot of histograms
library(lattice)
histogram(~ Value | Group,
          data=Data,
          layout=c(1,2)      #  columns and rows of individual plots
          )
 
 

Histograms for each popula on in a two-sample t-test. For the t-test to be valid, the
data in each popula on should be approximately normal. If the distribu ons are
different, minimally Welch’s t-test should be used. If the data are not normal or the
distribu ons are different, a non-parametric test like Mann-Whitney U-test or
permuta on test may be appropriate.

Box plots
 
boxplot(Value ~ Group,
        data = Data,
        names=c("2 pm","5 pm"),
        ylab="Value")
 
 Box plots of two popula ons from a two-sample t-test.
 
#     #     #
 
 
Similar tests
Welch’s t-test is discussed below. The paired t-test and signed-rank test are discussed in this book in their
own chapters. Analysis of variance (anova) is discussed in several subsequent chapters.
As non-parametric alternatives, the Mann–Whitney U-test and the permutation test for two independent
samples are discussed in the chapter Mann–Whitney and Two-sample Permutation Test.

Welch’s t-test
Welch’s t-test is shown above in the “Example” section (“Two sample unpaired t-test”). It is invoked with
the var.equal=FALSE option in the t.test function.

How to do the test

The SAS example from the Handbook is shown above in the “Example” section.

Power analysis
Power analysis for t-test
 
### --------------------------------------------------------------
### Power analysis, t-test, wide feet, p. 131
### --------------------------------------------------------------
M1  = 100.6                      # Mean for sample 1
M2  = 103.6                      # Mean for sample 2
S1  =  5.26                      # Std dev for sample 1
S2  =  5.26                      # Std dev for sample 2
Cohen.d = (M1 - M2)/sqrt(((S1^2) + (S2^2))/2) 
                                        
library(pwr)
                                  
pwr.t.test(
       n = NULL,                   # Observations in _each_ group
       d = Cohen.d,           
       sig.level = 0.05,           # Type I probability
       power = 0.90,               # 1 minus Type II probability
       type = "two.sample",        # Change for one- or two-sample
       alternative = "two.sided")
 
     Two-sample t test power calculation
 
              n = 65.57875     # Number for each group
 
#     #     #
 

©2015 by Salvatore S. Mangia ico.

Rutgers Cooperative Extension, New Brunswick, NJ.
 Organization of statistical tests and selection of examples for these tests ©2014 by John H. McDonald. Used with
permission.
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Citation:
Mangia ico, S.S. 2015. An R Companion for the Handbook of Biological Statistics, version 1.3.2.
rcompanion.org/rcompanion/. (Pdf version: rcompanion.org/documents/RCompanionBioStatistics.pdf.)