MTH 361 A/B SP23 (University of Portland): Lab 2 R Studio Cloud

Content Source: OpenIntro Statistics (4th edition) by David Diez, Mine Cetinkaya-Rundel, and Christopher Barr.

Getting Started

Load packages

In this lab, we will explore and visualize the data using the tidyverse suite of packages. The data can be found in the companion package for OpenIntro labs, openintro.

Let’s load the packages.

library(tidyverse)
library(openintro)

Creating a reproducible lab report

To create your new lab report, in RStudio, go to New File -> R Markdown… Then, choose From Template and then choose Lab Report for OpenIntro Statistics Labs from the list of templates.

I. Probability

The Hot Hand

Basketball players who make several baskets in succession are described as having a hot hand. Fans and players have long believed in the hot hand phenomenon, which refutes the assumption that each shot is independent of the next. However, a 1985 paper by Gilovich, Vallone, and Tversky collected evidence that contradicted this belief and showed that successive shots are independent events. This paper started a great controversy that continues to this day, as you can see by Googling hot hand basketball.

We do not expect to resolve this controversy today. However, in this lab we’ll apply one approach to answering questions like this. The goals for this lab are to (1) think about the effects of independent and dependent events, (2) learn how to simulate shooting streaks in R, and (3) to compare a simulation to actual data in order to determine if the hot hand phenomenon appears to be real.

Data

Your investigation will focus on the performance of one player: Kobe Bryant of the Los Angeles Lakers. His performance against the Orlando Magic in the 2009 NBA Finals earned him the title Most Valuable Player and many spectators commented on how he appeared to show a hot hand. The data file we’ll use is called kobe_basket.

glimpse(kobe_basket)

This data frame contains 133 observations and 6 variables, where every row records a shot taken by Kobe Bryant. The shot variable in this dataset indicates whether the shot was a hit (H) or a miss (M).

Just looking at the string of hits and misses, it can be difficult to gauge whether or not it seems like Kobe was shooting with a hot hand. One way we can approach this is by considering the belief that hot hand shooters tend to go on shooting streaks. For this lab, we define the length of a shooting streak to be the number of consecutive baskets made until a miss occurs.

For example, in Game 1 Kobe had the following sequence of hits and misses from his nine shot attempts in the first quarter:

\[ \textrm{H M | M | H H M | M | M | M} \]

You can verify this by viewing the first 9 rows of the data in the data viewer.

Within the nine shot attempts, there are six streaks, which are separated by a “|” above. Their lengths are one, zero, two, zero, zero, zero (in order of occurrence).

  1. What does a streak length of 1 mean, i.e. how many hits and misses are in a streak of 1? What about a streak length of 0?

Counting streak lengths manually for all 133 shots would get tedious, so we’ll use the custom function calc_streak to calculate them, and store the results in a data frame called kobe_streak as the length variable.

kobe_streak <- calc_streak(kobe_basket$shot)

We can then take a look at the distribution of these streak lengths.

ggplot(data = kobe_streak, aes(x = length)) +
  geom_bar()
  1. Describe the distribution of Kobe’s streak lengths from the 2009 NBA finals. What was his typical streak length? How long was his longest streak of baskets? Make sure to include the accompanying plot in your answer.

Compared to What?

We’ve shown that Kobe had some long shooting streaks, but are they long enough to support the belief that he had a hot hand? What can we compare them to?

To answer these questions, let’s return to the idea of independence. Two processes are independent if the outcome of one process doesn’t effect the outcome of the second. If each shot that a player takes is an independent process, having made or missed your first shot will not affect the probability that you will make or miss your second shot.

A shooter with a hot hand will have shots that are not independent of one another. Specifically, if the shooter makes his first shot, the hot hand model says he will have a higher probability of making his second shot.

Let’s suppose for a moment that the hot hand model is valid for Kobe. During his career, the percentage of time Kobe makes a basket (i.e. his shooting percentage) is about 45%, or in probability notation,

\[ P(\textrm{shot 1 = H}) = 0.45 \]

If he makes the first shot and has a hot hand (not independent shots), then the probability that he makes his second shot would go up to, let’s say, 60%,

\[ P(\textrm{shot 2 = H} \, | \, \textrm{shot 1 = H}) = 0.60 \]

As a result of these increased probabilities, you’d expect Kobe to have longer streaks. Compare this to the skeptical perspective where Kobe does not have a hot hand, where each shot is independent of the next. If he hit his first shot, the probability that he makes the second is still 0.45.

\[ P(\textrm{shot 2 = H} \, | \, \textrm{shot 1 = H}) = 0.45 \]

In other words, making the first shot did nothing to effect the probability that he’d make his second shot. If Kobe’s shots are independent, then he’d have the same probability of hitting every shot regardless of his past shots: 45%.

Now that we’ve phrased the situation in terms of independent shots, let’s return to the question: how do we tell if Kobe’s shooting streaks are long enough to indicate that he has a hot hand? We can compare his streak lengths to someone without a hot hand: an independent shooter.

Simulations in R

While we don’t have any data from a shooter we know to have independent shots, that sort of data is very easy to simulate in R. In a simulation, you set the ground rules of a random process and then the computer uses random numbers to generate an outcome that adheres to those rules. As a simple example, you can simulate flipping a fair coin with the following.

coin_outcomes <- c("heads", "tails")
sample(coin_outcomes, size = 1, replace = TRUE)

The vector coin_outcomes can be thought of as a hat with two slips of paper in it: one slip says heads and the other says tails. The function sample draws one slip from the hat and tells us if it was a head or a tail.

Run the second command listed above several times. Just like when flipping a coin, sometimes you’ll get a heads, sometimes you’ll get a tails, but in the long run, you’d expect to get roughly equal numbers of each.

If you wanted to simulate flipping a fair coin 100 times, you could either run the function 100 times or, more simply, adjust the size argument, which governs how many samples to draw (the replace = TRUE argument indicates we put the slip of paper back in the hat before drawing again). Save the resulting vector of heads and tails in a new object called sim_fair_coin.

sim_fair_coin <- sample(coin_outcomes, size = 100, replace = TRUE)

To view the results of this simulation, type the name of the object and then use table to count up the number of heads and tails.

sim_fair_coin
table(sim_fair_coin)

Since there are only two elements in coin_outcomes, the probability that we “flip” a coin and it lands heads is 0.5. Say we’re trying to simulate an unfair coin that we know only lands heads 20% of the time. We can adjust for this by adding an argument called prob, which provides a vector of two probability weights.

sim_unfair_coin <- sample(coin_outcomes, size = 100, replace = TRUE, 
                          prob = c(0.2, 0.8))

prob=c(0.2, 0.8) indicates that for the two elements in the outcomes vector, we want to select the first one, heads, with probability 0.2 and the second one, tails with probability 0.8. Another way of thinking about this is to think of the outcome space as a bag of 10 chips, where 2 chips are labeled “head” and 8 chips “tail”. Therefore at each draw, the probability of drawing a chip that says “head”” is 20%, and “tail” is 80%.

  1. In your simulation of flipping the unfair coin 100 times, how many flips came up heads? Include the code for sampling the unfair coin in your response. Since the markdown file will run the code, and generate a new sample each time you Knit it, you should also “set a seed” before you sample. Read more about setting a seed below.

A note on setting a seed: Setting a seed will cause R to select the same sample each time you knit your document. This will make sure your results don’t change each time you knit, and it will also ensure reproducibility of your work (by setting the same seed it will be possible to reproduce your results). You can set a seed like this:

set.seed(35797)                 # make sure to change the seed

The number above is completely arbitraty. If you need inspiration, you can use your ID, birthday, or just a random string of numbers. The important thing is that you use each seed only once in a document. Remember to do this before you sample in the exercise above.

In a sense, we’ve shrunken the size of the slip of paper that says “heads”, making it less likely to be drawn, and we’ve increased the size of the slip of paper saying “tails”, making it more likely to be drawn. When you simulated the fair coin, both slips of paper were the same size. This happens by default if you don’t provide a prob argument; all elements in the outcomes vector have an equal probability of being drawn.

If you want to learn more about sample or any other function, recall that you can always check out its help file.

?sample

Simulating the Independent Shooter

Simulating a basketball player who has independent shots uses the same mechanism that you used to simulate a coin flip. To simulate a single shot from an independent shooter with a shooting percentage of 50% you can type

shot_outcomes <- c("H", "M")
sim_basket <- sample(shot_outcomes, size = 1, replace = TRUE)

To make a valid comparison between Kobe and your simulated independent shooter, you need to align both their shooting percentage and the number of attempted shots.

  1. What change needs to be made to the sample function so that it reflects a shooting percentage of 45%? Make this adjustment, then run a simulation to sample 133 shots. Assign the output of this simulation to a new object called sim_basket.

Note that we’ve named the new vector sim_basket, the same name that we gave to the previous vector reflecting a shooting percentage of 50%. In this situation, R overwrites the old object with the new one, so always make sure that you don’t need the information in an old vector before reassigning its name.

With the results of the simulation saved as sim_basket, you have the data necessary to compare Kobe to our independent shooter.

Both data sets represent the results of 133 shot attempts, each with the same shooting percentage of 45%. We know that our simulated data is from a shooter that has independent shots. That is, we know the simulated shooter does not have a hot hand.

More Practice

Comparing Kobe Bryant to the Independent Shooter

  1. Using calc_streak, compute the streak lengths of sim_basket, and save the results in a data frame called sim_streak.

  2. Describe the distribution of streak lengths. What is the typical streak length for this simulated independent shooter with a 45% shooting percentage? How long is the player’s longest streak of baskets in 133 shots? Make sure to include a plot in your answer.

  3. If you were to run the simulation of the independent shooter a second time, how would you expect its streak distribution to compare to the distribution from the question above? Exactly the same? Somewhat similar? Totally different? Explain your reasoning.

  4. How does Kobe Bryant’s distribution of streak lengths compare to the distribution of streak lengths for the simulated shooter? Using this comparison, do you have evidence that the hot hand model fits Kobe’s shooting patterns? Explain.

II. The Normal Distribution

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.

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)
head(fastfood)
## # A tibble: 6 × 17
##   restaur…¹ item  calor…² cal_fat total…³ sat_fat trans…⁴ chole…⁵ sodium total…⁶
##   <chr>     <chr>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>  <dbl>   <dbl>
## 1 Mcdonalds Arti…     380      60       7       2     0        95   1110      44
## 2 Mcdonalds Sing…     840     410      45      17     1.5     130   1580      62
## 3 Mcdonalds Doub…    1130     600      67      27     3       220   1920      63
## 4 Mcdonalds Gril…     750     280      31      10     0.5     155   1940      62
## 5 Mcdonalds Cris…     920     410      45      12     0.5     120   1980      81
## 6 Mcdonalds Big …     540     250      28      10     1        80    950      46
## # … with 7 more variables: fiber <dbl>, sugar <dbl>, protein <dbl>,
## #   vit_a <dbl>, vit_c <dbl>, calcium <dbl>, salad <chr>, and abbreviated
## #   variable names ¹​restaurant, ²​calories, ³​total_fat, ⁴​trans_fat,
## #   ⁵​cholesterol, ⁶​total_carb

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?

The normal distribution

In your description of the distributions, did you use words like bell-shaped or 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")
## Warning: The dot-dot notation (`..density..`) was deprecated in ggplot2 3.4.0.
## ℹ Please use `after_stat(density)` instead.

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 calories from fat. 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?

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 dataframe, it can be put directly into the sample argument and the data argument can be dropped.)

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 from fat are nearly normal?

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

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)

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))

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?

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?

  2. 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?

  3. 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.

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