Response variable and explanatory variable

• We conduct an experiment, where we at random choose 50 IT-companies and 50 service companies and measure their profit ratio. Is there association between company type (IT/service) and profit ratio?
• In other words we compare samples from 2 different populations. For each company we register:
  • The binary variable company type, which is called the explanatory variable and divides data in 2 groups.
  • The quantitative variable profit ratio, which is called the response variable.

Dependent/independent samples

• In the example with profit ratio of 50 IT-companies and 50 service companies we have independent samples, since the same company cannot be in both groups.
• Now, think of another type of experiment, where we at random choose 50 IT-companies and measure their profit ratio in both 2009 and 2010. Then we may be interested in whether there is association between year and profit ratio?
• In this example we have dependent samples, since the same company is in both groups.
• Dependent samples may also be referred to as paired samples.

Comparison of two means (Independent samples)

• We consider the situation, where we have two quantitative samples:
  • Population 1 has mean \(\mu_1\), which is estimated by \(\hat{\mu}_1=\bar{y}_1\) based on a sample of size \(n_1\).
  • Population 2 has mean \(\mu_2\), which is estimated by \(\hat{\mu}_2=\bar{y}_2\) based on a sample of size \(n_2\).
  • We are interested in the difference \(\mu_2-\mu_1\), which is estimated by \(d=\bar{y}_2-\bar{y}_1\).
  • Assume that we can find the estimated standard error \(se_d\) of the difference and that this has degrees of freedom \(df\).
  • Assume that the samples either are large or come from a normal population.
• Then we can construct a
  • confidence interval for the unknown population difference of means \(\mu_2-\mu_1\) by \[ (\bar{y}_2-\bar{y}_1)\pm t_{crit}se_d, \] where the critical \(t\)-score, \(t_{crit}\), determines the confidence level.
  • significance test:
    • for the null hypothesis \(H_0:\ \mu_2-\mu_1=0\) and alternative hypothesis \(H_a:\ \mu_2-\mu_1\neq 0\).
    • which uses the test statistic: \(t_{obs} = \frac{(\bar{y}_2-\bar{y}_1) - 0}{se_d}\), that has to be evaluated in a \(t\)-distribution with \(df\) degrees of freedom.

Comparison of two means (Independent samples)

• In the independent samples situation it can be shown that \[ se_d=\sqrt{se_1^2+se_2^2}, \] where \(se_1\) and \(se_2\) are estimated standard errors for the sample means in populations 1 and 2, respectively.
• We recall, that for these we have \(se=\frac{s}{\sqrt{n}}\), i.e. \[ se_d=\sqrt{\frac{s_1^2}{n_1}+\frac{s_2^2}{n_2}}, \] where \(s_1\) and \(s_2\) are estimated standard deviations for population 1 and 2, respectively.
• The degrees of freedom \(df\) for \(se_d\) can be estimated by a complicated formula, which we will not present here.
• For the confidence interval and the significance test we note that:
  • If both \(n_1\) and \(n_2\) are above 30, then we can use the standard normal distribution (\(z\)-score) rather than the \(t\)-distribution (\(t\)-score).
  • If \(n_1\) or \(n_2\) are below 30, then we let R calculate the degrees of freedom and \(p\)-value/confidence interval.

Example: Comparing two means (independent samples)

We return to the Chile data. We study the association between the variables sex and statusquo (scale of support for the status-quo). So, we will perform a significance test to test for difference in the mean of statusquo for male and females.

Chile <- read.delim("https://asta.math.aau.dk/datasets?file=Chile.txt")
library(mosaic)
fv <- favstats(statusquo ~ sex, data = Chile)
fv

##   sex   min     Q1 median    Q3  max    mean    sd    n missing
## 1   F -1.80 -0.975  0.121 1.033 2.02  0.0657 1.003 1368      11
## 2   M -1.74 -1.032 -0.216 0.861 2.05 -0.0684 0.993 1315       6

• Difference: \(d = 0.0657 - (-0.0684) = 0.1341\).
• Estimated standard deviations: \(s_1 = 1.0032\) (females) and \(s_2 = 0.9928\) (males).
• Sample sizes: \(n_1 = 1368\) and \(n_2 = 1315\).
• Estimated standard error of difference:  \(se_d = \sqrt{\frac{s_1^2}{n_1} + \frac{s_2^2}{n_2}} = \sqrt{\frac{1.0032^2}{1368} + \frac{0.9928^2}{1315}} = 0.0385\).
• Observed \(t\)-score for \(H_0:\ \mu_1-\mu_2=0\) is: \(\quad t_{obs} = \frac{d-0}{se_d} = \frac{0.1341}{0.0385} = 3.4786\).
• Since both sample sizes are “pretty large” (> 30), we can use the \(z\)-score instead of the \(t\)-score for finding the \(p\)-value (i.e. we use the standard normal distribution):

1 - pdist("norm", q = 3.4786, xlim = c(-4, 4))

## [1] 0.0002520202

• Then the \(p\)-value is \(2\cdot 0.00025 = 0.0005\), so we reject the null hypothesis.
• We can leave all the calculations to R by using t.test:

t.test(statusquo ~ sex, data = Chile)

## 
##  Welch Two Sample t-test
## 
## data:  statusquo by sex
## t = 3.4786, df = 2678.7, p-value = 0.0005121
## alternative hypothesis: true difference in means between group F and group M is not equal to 0
## 95 percent confidence interval:
##  0.05849179 0.20962982
## sample estimates:
## mean in group F mean in group M 
##      0.06570627     -0.06835453

• We recognize the \(t\)-score \(3.4786\) and the \(p\)-value \(0.0005\). The estimated degrees of freedom \(df = 2679\) is so large that we can not tell the difference between results obtained using \(z\)-score and \(t\)-score.

Comparison of two means: confidence interval (independent samples)

• We have already found all the ingredients to construct a confidence interval for \(\mu_2-\mu_1\):
  • \(d=\bar{y}_2-\bar{y}_1\) estimates \(\mu_2-\mu_1\).
  • \(se_d=\sqrt{\frac{s_1^2}{n_1}+\frac{s_2^2}{n_2}}\) estimates the standard error of \(d\).
• Then: \[ d\pm t_{crit}se_d \] is a confidence interval for \(\mu_2-\mu_1\).
• The critical \(t\)-score, \(t_{crit}\) is chosen corresponding to the wanted confidence level. If \(n_1\) and \(n_2\) both are greater than 30, then \(t_{crit} = 2\) yields a confidence level of approximately 95%.

Comparison of two means: paired \(t\)-test (dependent samples)

• Experiment:
  • You choose 32 students at random and measure their average reaction time in a driving simulator while they are listening to radio or audio books.
  • Later the same 32 students redo the simulated driving while talking on a cell phone.
• It is interesting to investigate whether or not the fact that you are actively participating in a conversation changes your average reaction time compared to when you are passively listening.
• So we have 2 samples corresponding to with/without phone. In this case we have dependent samples, since we have 2 measurement for each student.
• We use the following strategy for analysis:
  • For each student calculate the change in average reaction time with and without talking on the phone.
  • The changes \(d_1,d_2,\ldots,d_{32}\) are now considered as ONE sample from a population with mean \(\mu\).
  • Test the hypothesis \(H_0: \mu=0\) as usual (using a \(t\)-test for testing the mean as in the previous lecture).

Reaction time example

• Data is organized in a data frame with 3 variables:
  • student (integer – a simple id)
  • reaction_time (numeric – average reaction time in milliseconds)
  • phone (factor – yes/no indicating whether speaking on the phone)

reaction <- read.delim("https://asta.math.aau.dk/datasets?file=reaction.txt")
head(reaction, n = 3)

##   student reaction_time phone
## 1       1           604    no
## 2       2           556    no
## 3       3           540    no

Instead of doing manual calculations we let R perform the significance test (using t.test with paired = TRUE as our samples are paired/dependent):

yes <- subset(reaction, phone == "yes")
no  <- subset(reaction, phone == "no")
all(yes$student == no$student)

## [1] TRUE

reaction_paired <- data.frame(student = no$student, yes = yes$reaction_time, no = no$reaction_time)
t.test(reaction_paired$no, reaction_paired$yes, paired = TRUE)

## 
##  Paired t-test
## 
## data:  reaction_paired$no and reaction_paired$yes
## t = -5.4563, df = 31, p-value = 5.803e-06
## alternative hypothesis: true mean difference is not equal to 0
## 95 percent confidence interval:
##  -69.54814 -31.70186
## sample estimates:
## mean difference 
##         -50.625

• With a \(p\)-value of 0.0000058 we reject that speaking on the phone has no influence on the reaction time.

• To understand what is going on, we can manually find the reaction time difference for each student and do a one sample t-test on this difference:

reaction_paired$diff <- reaction_paired$yes - reaction_paired$no
head(reaction_paired)

##   student yes  no diff
## 1       1 636 604   32
## 2       2 623 556   67
## 3       3 615 540   75
## 4       4 672 522  150
## 5       5 601 459  142
## 6       6 600 544   56

t.test( ~ diff, data = reaction_paired)

## 
##  One Sample t-test
## 
## data:  diff
## t = 5.4563, df = 31, p-value = 5.803e-06
## alternative hypothesis: true mean is not equal to 0
## 95 percent confidence interval:
##  31.70186 69.54814
## sample estimates:
## mean of x 
##    50.625

Comparison of two proportions

• We consider the situation, where we have two qualitative samples and we investigate whether a given property is present or not:
  • Let the proportion of population 1 which has the property be \(\pi_1\), which is estimated by \(\hat{\pi}_1\) based on a sample of size \(n_1\).
  • Let the proportion of population 2 which has the property be \(\pi_2\), which is estimated by \(\hat{\pi}_2\) based on a sample of size \(n_2\).
  • We are interested in the difference \(\pi_2-\pi_1\), which is estimated by \(d=\hat{\pi}_2-\hat{\pi}_1\).
  • Assume that we can find the estimated standard error \(se_d\) of the difference.
• Then we can construct
  • an approximate confidence interval for the difference, \(\pi_2 - \pi_1\).
  • a significance test.

Comparison of two proportions: Independent samples

• In the situation where we have independent samples we know that \[ se_d=\sqrt{se_1^2+se_2^2}, \] where \(se_1\) and \(se_2\) are the estimated standard errors for the sample proportion in population 1 and 2, respectively.
• We recall, that these are given by \(se=\sqrt{\frac{\hat{\pi}(1-\hat{\pi})}{n}}\), i.e. \[ se_d = \sqrt{\frac{\hat{\pi}_1(1-\hat{\pi}_1)}{n_1}+\frac{\hat{\pi}_2(1-\hat{\pi}_2)}{n_2}}. \]
• A (approximate) confidence interval for \(\pi_2-\pi_1\) is obtained by the usual construction:
  \[ (\hat{\pi}_2-\hat{\pi}_1)\pm z_{crit}se_d, \] where the critical \(z\)-score determines the confidence level.

Approximate test for comparing two proportions (independent samples)

• We consider the null hypothesis \(H_0\): \(\pi_1=\pi_2\) (equivalently \(H_0: \pi_1 - \pi_2 = 0\)) and the alternative hypothesis \(H_a\): \(\pi_1 \neq \pi_2\).
• Assuming \(H_0\) is true, we have a common proportion \(\pi\), which is estimated by \[ \hat{\pi}=\frac{n_1\hat{\pi}_1+n_2\hat{\pi}_2}{n_1+n_2}, \] i.e. we aggregate the populations and calculate the relative frequency of the property (with other words: we estimate the proportion, \(\pi\), as if the two samples were one).
• Rather than using the estimated standard error of the difference from previous, we use the following that holds under \(H_0\): \[ se_0=\sqrt{\hat{\pi}(1-\hat{\pi})\left(\frac{1}{n_1}+\frac{1}{n_2}\right)} \]
• The observed test statistic/\(z\)-score for \(H_0\) is then: \[ z_{obs}=\frac{(\hat{\pi}_2-\hat{\pi}_1) - 0}{se_0}, \] which is evaluated in the standard normal distribution.
• The \(p\)-value is calculated in the usual way.

WARNING: The approximation is only good, when \(n_1\hat{\pi},\ n_1(1-\hat{\pi}),\ n_2\hat{\pi},\ n_2(1-\hat{\pi})\) all are greater than 5.

Example: Approximate confidence interval and test for comparing proportions

We return to the Chile dataset. We make a new binary variable indicating whether the person intends to vote no or something else (and we remember to tell R that it should think of this as a grouping variable, i.e. a factor):

Chile$voteNo <- relevel(factor(Chile$vote == "N"), ref = "TRUE")

We study the association between the variables sex and voteNo:

tab <- tally( ~ sex + voteNo, data = Chile, useNA = "no")
tab

##    voteNo
## sex TRUE FALSE
##   F  363   946
##   M  526   697

This gives us all the ingredients needed in the hypothesis test:

• Estimated proportion of men that vote no: \(\hat{\pi}_1=\frac{526}{526+697}=0.430\)
• Estimated proportion of women that vote no: \(\hat{\pi}_2=\frac{363}{363+946}=0.277\)

Example: Approximate confidence interval (cont.)

• Estimated difference:
  \[d=\hat{\pi}_2-\hat{\pi}_1=0.277-0.430=-0.153\]
• Standard error of difference:
  \[\begin{aligned}se_d&=\sqrt{\frac{\hat{\pi}_1(1-\hat{\pi}_1)}{n_1}+\frac{\hat{\pi}_2(1-\hat{\pi}_2)}{n_2}} \\ &= \sqrt{\frac{0.430(1-0.430)}{1223}+\frac{0.277(1-0.277)}{1309}}= 0.0188. \end{aligned}\]
• Approximate 95% confidence interval for difference:  \[d \pm 1.96 \cdot se_d = (-0.190, -0.116).\]

Example: \(p\)-value (cont.)

• Estimated common proportion:  \[\hat{\pi}=\frac{1223 \times 0.430 + 1309 \times 0.277}{1309+1223}=\frac{526 + 363}{1309+1223}=0.351.\]
• Standard error of difference when \(H_0:\ \pi_1=\pi_2\) is true: \[se_0=\sqrt{\hat{\pi}(1-\hat{\pi})\left(\frac{1}{n_1}+\frac{1}{n_2}\right)} = 0.0190.\]
• The observed test statistic/\(z\)-score:  \[z_{obs}=\frac{d}{se_0}=-8.06.\]
• The test for \(H_0\) against \(H_a: \pi_1\not=\pi_2\) yields a \(p\)-value that is practically zero, i.e. we can reject that the proportions are equal.

Automatic calculation in R

Chile2 <- subset(Chile, !is.na(voteNo))
prop.test(voteNo ~ sex, data = Chile2, correct = FALSE)

## 
##  2-sample test for equality of proportions without continuity correction
## 
## data:  tally(voteNo ~ sex)
## X-squared = 64.777, df = 1, p-value = 8.389e-16
## alternative hypothesis: two.sided
## 95 percent confidence interval:
##  -0.1896305 -0.1159275
## sample estimates:
##    prop 1    prop 2 
## 0.2773109 0.4300899

Fisher’s exact test

• If \(n_1\hat{\pi},\ n_1(1-\hat{\pi}),\ n_2\hat{\pi},\ n_2(1-\hat{\pi})\) are not all greater than 5, then the approximate test cannot be trusted. Instead you can use Fisher’s exact test:

fisher.test(tab)

## 
##  Fisher's Exact Test for Count Data
## 
## data:  tab
## p-value = 1.04e-15
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##  0.4292768 0.6021525
## sample estimates:
## odds ratio 
##  0.5085996

• Again the \(p\)-value is seen to be extremely small, so we definitely reject the null hypothesis of equal voteNo proportions for women and men.

Agresti: Overview of comparison of two groups