In this lab, you’ll investigate the probability distribution that is most central to statistics: the normal distribution. If you are confident that your data are nearly normal, that opens the door to many powerful statistical methods. Here we’ll use the graphical tools of R to assess the normality of our data and also learn how to generate random numbers from a normal distribution.

Getting Started

Load packages

In this lab, we will explore and visualize the data using the tidyverse suite of packages as well as the openintro package.

Let’s load the packages.

library(tidyverse)
library(openintro)

The data

This week you’ll be working with fast food data. This data set contains data on 515 menu items from some of the most popular fast food restaurants worldwide. Let’s take a quick peek at the first few rows of the data.

Either you can use glimpse like before, or head to do this.

library(tidyverse)
library(openintro)
data("fastfood", package='openintro')
head(fastfood)
## # A tibble: 6 × 17
##   restaurant item       calories cal_fat total_fat sat_fat trans_fat cholesterol
##   <chr>      <chr>         <dbl>   <dbl>     <dbl>   <dbl>     <dbl>       <dbl>
## 1 Mcdonalds  Artisan G…      380      60         7       2       0            95
## 2 Mcdonalds  Single Ba…      840     410        45      17       1.5         130
## 3 Mcdonalds  Double Ba…     1130     600        67      27       3           220
## 4 Mcdonalds  Grilled B…      750     280        31      10       0.5         155
## 5 Mcdonalds  Crispy Ba…      920     410        45      12       0.5         120
## 6 Mcdonalds  Big Mac         540     250        28      10       1            80
## # ℹ 9 more variables: sodium <dbl>, total_carb <dbl>, fiber <dbl>, sugar <dbl>,
## #   protein <dbl>, vit_a <dbl>, vit_c <dbl>, calcium <dbl>, salad <chr>

You’ll see that for every observation there are 17 measurements, many of which are nutritional facts.

You’ll be focusing on just three columns to get started: restaurant, calories, calories from fat.

Let’s first focus on just products from McDonalds and Dairy Queen.

mcdonalds <- fastfood %>%
  filter(restaurant == "Mcdonalds")
dairy_queen <- fastfood %>%
  filter(restaurant == "Dairy Queen")
  1. Make a plot (or plots) to visualize the distributions of the amount of calories from fat of the options from these two restaurants. How do their centers, shapes, and spreads compare?

Based on the visualizations, both of these plots appear to be right-skewed. Both have similar centers at approximately 200 calories. Mc’donalds has a higher max of above 1000 calories from fat compared to Dairy Queen which has a max of about 700 calories from fat.

ggplot(mcdonalds, aes(x = cal_fat)) + 
geom_histogram(binwidth = 100)   

ggplot(dairy_queen, aes(x=cal_fat)) +
geom_histogram(binwidth = 100)

The normal distribution

In your description of the distributions, did you use words like bell-shapedor normal? It’s tempting to say so when faced with a unimodal symmetric distribution.

To see how accurate that description is, you can plot a normal distribution curve on top of a histogram to see how closely the data follow a normal distribution. This normal curve should have the same mean and standard deviation as the data. You’ll be focusing on calories from fat from Dairy Queen products, so let’s store them as a separate object and then calculate some statistics that will be referenced later.

dqmean <- mean(dairy_queen$cal_fat)
dqsd   <- sd(dairy_queen$cal_fat)

Next, you make a density histogram to use as the backdrop and use the lines function to overlay a normal probability curve. The difference between a frequency histogram and a density histogram is that while in a frequency histogram the heights of the bars add up to the total number of observations, in a density histogram the areas of the bars add up to 1. The area of each bar can be calculated as simply the height times the width of the bar. Using a density histogram allows us to properly overlay a normal distribution curve over the histogram since the curve is a normal probability density function that also has area under the curve of 1. Frequency and density histograms both display the same exact shape; they only differ in their y-axis. You can verify this by comparing the frequency histogram you constructed earlier and the density histogram created by the commands below.

ggplot(data = dairy_queen, aes(x = cal_fat)) +
        geom_blank() +
        geom_histogram(aes(y = ..density..)) +
        stat_function(fun = dnorm, args = c(mean = dqmean, sd = dqsd), col = "tomato")

After initializing a blank plot with geom_blank(), the ggplot2 package (within the tidyverse) allows us to add additional layers. The first layer is a density histogram. The second layer is a statistical function – the density of the normal curve, dnorm. We specify that we want the curve to have the same mean and standard deviation as the column of fat calories. The argument col simply sets the color for the line to be drawn. If we left it out, the line would be drawn in black.

  1. Based on the this plot, does it appear that the data follow a nearly normal distribution?

This plot is close to be a normal distribution but it is slightly skewed to the right. This would lead me to conclude that yes, it is a nearly normal distribution

Evaluating the normal distribution

Eyeballing the shape of the histogram is one way to determine if the data appear to be nearly normally distributed, but it can be frustrating to decide just how close the histogram is to the curve. An alternative approach involves constructing a normal probability plot, also called a normal Q-Q plot for “quantile-quantile”.

ggplot(data = dairy_queen, aes(sample = cal_fat)) + geom_line(stat = "qq")

This time, you can use the geom_line() layer, while specifying that you will be creating a Q-Q plot with the stat argument. It’s important to note that here, instead of using x instead aes(), you need to use sample.

The x-axis values correspond to the quantiles of a theoretically normal curve with mean 0 and standard deviation 1 (i.e., the standard normal distribution). The y-axis values correspond to the quantiles of the original unstandardized sample data. However, even if we were to standardize the sample data values, the Q-Q plot would look identical. A data set that is nearly normal will result in a probability plot where the points closely follow a diagonal line. Any deviations from normality leads to deviations of these points from that line.

The plot for Dairy Queen’s calories from fat shows points that tend to follow the line but with some errant points towards the upper tail. You’re left with the same problem that we encountered with the histogram above: how close is close enough?

A useful way to address this question is to rephrase it as: what do probability plots look like for data that I know came from a normal distribution? We can answer this by simulating data from a normal distribution using rnorm.

sim_norm <- rnorm(n = nrow(dairy_queen), mean = dqmean, sd = dqsd)

The first argument indicates how many numbers you’d like to generate, which we specify to be the same number of menu items in the dairy_queen data set using the nrow() function. The last two arguments determine the mean and standard deviation of the normal distribution from which the simulated sample will be generated. You can take a look at the shape of our simulated data set, sim_norm, as well as its normal probability plot.

  1. Make a normal probability plot of sim_norm. Do all of the points fall on the line? How does this plot compare to the probability plot for the real data? (Since sim_norm is not a data frame, it can be put directly into the sample argument and the data argument can be dropped.)
ggplot(data = NULL, aes(sample = sim_norm)) +
geom_line(stat = "qq")

qqnorm(sim_norm)

I created a plot for sim_norm and all of the points did not fall on the line. This probability plot is very similar to the plot for the real data as it has a fairly normal distribution but it slightly skews to the right.

Even better than comparing the original plot to a single plot generated from a normal distribution is to compare it to many more plots using the following function. It shows the Q-Q plot corresponding to the original data in the top left corner, and the Q-Q plots of 8 different simulated normal data. It may be helpful to click the zoom button in the plot window.

qqnormsim(sample = cal_fat, data = dairy_queen)

  1. Does the normal probability plot for the calories from fat look similar to the plots created for the simulated data? That is, do the plots provide evidence that the calories are nearly normal?

In this this case the normal probability plot for calories from fat does look similar to the simulated data. This plot confirms our thesis that the calories are nearly normal.

  1. Using the same technique, determine whether or not the calories from McDonald’s menu appear to come from a normal distribution.

Using the same technique from above I believe the calories from McDonald’s menu appears to be close to a normal distribution but not quite. The textbook states that a line that curves upward at the top it is slightly skewed to the right.

qqnormsim(sample = cal_fat, data = mcdonalds)

qqnorm(sim_norm)

Normal probabilities

Okay, so now you have a slew of tools to judge whether or not a variable is normally distributed. Why should you care?

It turns out that statisticians know a lot about the normal distribution. Once you decide that a random variable is approximately normal, you can answer all sorts of questions about that variable related to probability. Take, for example, the question of, “What is the probability that a randomly chosen Dairy Queen product has more than 600 calories from fat?”

If we assume that the calories from fat from Dairy Queen’s menu are normally distributed (a very close approximation is also okay), we can find this probability by calculating a Z score and consulting a Z table (also called a normal probability table). In R, this is done in one step with the function pnorm().

1 - pnorm(q = 600, mean = dqmean, sd = dqsd)
## [1] 0.01501523

Note that the function pnorm() gives the area under the normal curve below a given value, q, with a given mean and standard deviation. Since we’re interested in the probability that a Dairy Queen item has more than 600 calories from fat, we have to take one minus that probability.

Assuming a normal distribution has allowed us to calculate a theoretical probability. If we want to calculate the probability empirically, we simply need to determine how many observations fall above 600 then divide this number by the total sample size.

dairy_queen %>% 
  filter(cal_fat > 600) %>%
  summarise(percent = n() / nrow(dairy_queen))
## # A tibble: 1 × 1
##   percent
##     <dbl>
## 1  0.0476

Although the probabilities are not exactly the same, they are reasonably close. The closer that your distribution is to being normal, the more accurate the theoretical probabilities will be.

  1. Write out two probability questions that you would like to answer about any of the restaurants in this dataset. Calculate those probabilities using both the theoretical normal distribution as well as the empirical distribution (four probabilities in all). Which one had a closer agreement between the two methods?

Probability that a a randomly chosen item is above 300 calories

pnorm(300, dqmean, dqsd)
## [1] 0.5997007
dairy_queen %>%
  filter(cal_fat > 300) %>%
  summarise(percent = n() / nrow(dairy_queen))
## # A tibble: 1 × 1
##   percent
##     <dbl>
## 1   0.333

Probability that a randomly chosen food item is between 300 and 500 calories

pnorm(500, dqmean, dqsd) - pnorm(300, dqmean, dqsd)
## [1] 0.3373713
dairy_queen %>%
  filter(cal_fat < 500 & cal_fat > 300) %>%
  summarise(percent = n() / nrow(dairy_queen)) +
  pnorm(500, dqmean, dqsd) - pnorm(300, dqmean, dqsd)
##     percent
## 1 0.5992761

Pr{Y < 500 & Y > 300} is in closer agreement to the probability using the empirical distribution.

More Practice

  1. Now let’s consider some of the other variables in the dataset. Out of all the different restaurants, which ones’ distribution is the closest to normal for sodium?
normality_test_results <- fastfood %>%
group_by(restaurant) %>%
summarise(shapiro_p_value = shapiro.test(sodium)$p.value)

normal_restaurants <- normality_test_results %>%
filter(shapiro_p_value > 0.05)

print(normal_restaurants)
## # A tibble: 2 × 2
##   restaurant  shapiro_p_value
##   <chr>                 <dbl>
## 1 Arbys                 0.199
## 2 Burger King           0.133

Based on my analysis Burger King has the closest distribution to normal for sodium, followed by a close #2 of Arbys. I used a test that is commonly used for normality which is the Shapiro-Wilk test.

  1. Note that some of the normal probability plots for sodium distributions seem to have a stepwise pattern. why do you think this might be the case?

I believe these sodium distributions may have a stepwise pattern due to the fact that some food items may be popular than others and some may have a higher sodium content then others. This in turn creates a “granularity” that appears “step-wise”.

  1. As you can see, normal probability plots can be used both to assess normality and visualize skewness. Make a normal probability plot for the total carbohydrates from a restaurant of your choice. Based on this normal probability plot, is this variable left skewed, symmetric, or right skewed? Use a histogram to confirm your findings.
ggplot(mcdonalds, aes(sample = total_carb)) +
geom_line(stat = "qq")

qqnormsim(sample = total_carb, data = mcdonalds)

ggplot(mcdonalds, aes(x = total_carb)) +
geom_histogram(binwidth = 5)

Based on this normal probability plot, I would say it is slightly skewed right. I will create a distribution with a normal distribution line to check whether this is accurate.

mean_carb <- mean(mcdonalds$total_carb)
sd_carb <- sd(mcdonalds$total_carb)

ggplot(mcdonalds, aes(x = total_carb)) +
geom_histogram(binwidth = 5) +
stat_function(fun = dnorm, args = c(mean = mean_carb, sd = sd_carb), col = "tomato") + 
xlab("Total Carbohydrates") +
ylab("Frequency")