---
title: "Matched pairs"
editor:
markdown:
wrap: 72
---
## Matched pairs
Some data:
![](Screenshot_2019-04-26_13-41-29.png){width="679"}
## Matched pairs 1/2
- Data are comparison of 2 drugs for effectiveness at reducing pain.
- 12 subjects (cases) were arthritis sufferers
- Response is #hours of pain relief from each drug.
- In reading example, each child tried only one reading method.
- But here, each subject tried out both drugs, giving us two
measurements.
- Possible because, if you wait long enough, one drug has no influence
over effect of other.
## Matched pairs 2/2
- Advantage: focused comparison of drugs. Compare one drug with
another on same person, removes a lot of variability due to
differences between people.
- Matched pairs, requires different analysis.
- Design: randomly choose 6 of 12 subjects to get drug A first, other
6 get drug B first.
## Packages
```{r}
library(tidyverse)
library(smmr) # for a sign test later
```
## Reading the data
Values aligned in columns:
```{r inference-4b-R-1}
my_url <-
"http://ritsokiguess.site/datafiles/analgesic.txt"
pain <- read_table(my_url)
pain
glimpse(pain)
```
## Paired *t*-test
```{r inference-4b-R-3}
with(pain, t.test(druga, drugb, paired = TRUE))
```
- P-value is 0.053.
- Not quite evidence of difference between drugs.
## t-testing the differences
- Likewise, you can calculate the differences yourself and then do a
1-sample t-test on them.
```{r inference-4b-R-4}
pain %>% mutate(diff = druga - drugb) -> pain
pain
```
## t-test on the differences
- then throw them into t.test, testing that the mean is zero, with
same result as before:
```{r inference-4b-R-5}
with(pain, t.test(diff, mu = 0))
```
- Same P-value (0.053) and conclusion.
## Assessing normality
- 1-sample and 2-sample t-tests assume (each) group normally
distributed.
- Matched pairs analyses assume (theoretically) that differences
normally distributed.
- How to assess normality? A normal quantile plot.
## The normal quantile plot (of differences)
```{r inference-4b-R-6, fig.height=4}
ggplot(pain,aes(sample=diff))+stat_qq()+stat_qq_line()
```
- Points should follow the straight line. Bottom left one way off, so
normality questionable here: outlier.
## What to do instead?
- Matched pairs $t$-test based on one sample of differences
- the differences not normal (enough)
- so do *sign test* on differences, null median 0:
```{r inference-4b-R-7}
sign_test(pain, diff, 0)
```
## Did we need to worry about that outlier?
Bootstrap sampling distribution of sample mean differences:
```{r}
tibble(sim = 1:10000) %>%
rowwise() %>%
mutate(my_sample = list(sample(pain$diff, replace = TRUE))) %>%
mutate(my_mean = mean(my_sample)) %>%
ggplot(aes(sample = my_mean)) + stat_qq() + stat_qq_line()
```
Yes we did; this is clearly skewed left and not normal.
## Comments
- no evidence of any difference between drugs (P-value 0.1460)
- in $t$-test, the low outlier difference pulled mean difference
downward and made it look more negative than it should have been
- therefore, there really isn't any difference between the drugs.