--- title: "STAT 801A Lab 2: Quarto and Probability Distributions" author: "Insert Name" date: today format: html: number-sections: false editor: visual execute: warning: false --- # Quarto An R script (.R) holds only code. A Quarto document (.qmd) holds code, output, and writing in one file. You "render" the file and Quarto runs every piece of R code, captures the results, and stitches everything into a finished HTML page, PDF, or Word document. To learn more about Quarto see . ## Text Formatting \# Level 1 heading \## Level 2 heading \### Level 3 heading (and so on) \*italic\* and \*\*bold\*\* and \`code style\` \- bullet point 1\. numbered item 2\. another item Make sure to leave a blank line between paragraphs. Two paragraphs jammed together with no blank line will render as one. ## Code chunks We can run normal R code with code chunks. You can insert one with `Ctrl + Alt + I` (`command + option + I` on macOS) or you can insert one manually ```{r} 2 + 2 ``` ### Chunk options Options go inside the chunk on lines starting with `#|`. The space after `#|` is required. ```{r} #| echo: true #| eval: true mean(c(82, 91, 76, 88, 95)) ``` ## Inline code To drop a computed number into a sentence, use `r "code"` wrapped inbetween backticks. ```{r} scores <- c(82, 91, 76, 88, 95) ``` The mean score was `r (mean(scores))` ## Rendering Click the **Render** button at the top of the editor (or press `Ctrl + Shift + K`, or `Command + Shift + K` on macOS). RStudio saves the file, runs all the code from top to bottom in a fresh R session, and opens the result in whatever format is specified # Math Equations with LaTeX Quarto renders mathematical notation using LaTeX syntax. ## Symbol reference | You want | You type | Result | |------------------------|------------------------|------------------------| | Greek letters | `$\mu$ $\sigma$ $\lambda$ $\alpha$ $\beta$` | $\mu$ $\sigma$ $\lambda$ $\alpha$ $\beta$ | | Capital Greek | `$\Sigma$ $\Delta$ $\Phi$` | $\Sigma$ $\Delta$ $\Phi$ | | Subscript | `$x_1$` and `$x_{10}$` | $x_1$ and $x_{10}$ | | Superscript | `$x^2$` and `$e^{-\lambda}$` | $x^2$ and $e^{-\lambda}$ | | Fraction | `$\frac{a}{b}$` | $\frac{a}{b}$ | | Square root | `$\sqrt{x}$` and `$\sqrt[3]{x}$` | $\sqrt{x}$ and $\sqrt[3]{x}$ | | Summation | `$\sum_{i=1}^{n} x_i$` | $\sum_{i=1}^{n} x_i$ | | Product | `$\prod_{i=1}^{n} x_i$` | $\prod_{i=1}^{n} x_i$ | | Integral | `$\int_{-\infty}^{\infty} f(x)\,dx$` | $\int_{-\infty}^{\infty} f(x)\,dx$ | | Binomial coefficient | `$\binom{n}{k}$` | $\binom{n}{k}$ | | Bar / hat | `$\bar{x}$` and `$\hat{p}$` | $\bar{x}$ and $\hat{p}$ | | Inequalities | `$\leq$ $\geq$ $\neq$ $\approx$` | $\leq$ $\geq$ $\neq$ $\approx$ | | Plus/minus | `$\pm$` | $\pm$ | | Distributed as | `$X \sim N(\mu, \sigma^2)$` | $X \sim N(\mu, \sigma^2)$ | Wrap math in single dollar signs to put it in a sentence, or double dollar signs to put it on its own centered line. # ggplot2 ```{r} #install.packages("ggplot2) library(ggplot2) ``` Every ggplot needs three things, and layers are joined with a +: 1. Data - a data frame. 2. Aesthetic mapping - which column goes on which axis, written inside aes(). 3. A geom - what type of plot is drawn ```{r} ggplot(data = mtcars, aes(x = wt, y = mpg)) + geom_point() ``` ## Common geoms | Geom | Draws | Typically needs | |------------------|----------------------------|-----------------| | geom_point() | Scatterplot | x and y | | geom_line() | Connected line | x and y | | geom_col() | Bars at heights you supply | x and y | | geom_histogram() | Histogram | x only | | geom_boxplot() | Boxplot | x and y | | geom_smooth() | Trend line | x and y | ## Labels and themes labs() sets the title and axis labels. A theme\_\*() function changes the overall look. ```{r} ggplot(data = mtcars, aes(x = wt, y = mpg)) + geom_point() + labs(x = "Weight",y = "Miles per Gallon") + theme_minimal() ``` ## Mapping color vs. setting color Inside aes(), a color is mapped to a variable, so it changes from point to point and a legend appears Outside aes(), a color is set to one fixed value for everything Generally, if the appearance should depend on the data, it goes inside aes(). If it is just a style choice you are making, it goes outside. ```{r} ggplot(data = mtcars, aes(x = mpg)) + geom_histogram(bins=10,color = "black",fill="lightblue") ``` ```{r} ggplot(data = mtcars, aes(x = wt, y = mpg, color = factor(cyl))) + geom_point() + labs(x = "Weight",y = "Miles per Gallon") + theme_minimal() ``` # Probability Distributions in R A **probability distribution** is a rule that tells you how likely each possible outcome is. Discrete: - Binomial - Number of successes in a fixed number of trials - Poisson - Count of events occurring in a fixed interval of time or space Continuous - Normal - Continuous distribution with a symmetric, bell-shaped curve When we assume a random variable follows a particular probability distribution, we can calculate the probability that the random variable takes a particular value or falls within a particular range of values. | Wording | Distribution | |----------------------------------------------------------|--------------| | "out of 20 coin flips," "12 questions," "10 free throws" | Binomial | | "what proportion of trials succeed" | Binomial | | "an average of 4.5 per hour," "3.2 per month" | Poisson | | "how many arrive," "how many occur" | Poisson | | "normally distributed," "bell-shaped" | Normal | | "mean of 500 hours with a standard deviation of 45" | Normal | ## Notation You will see distributions written in shorthand. The symbol $\sim$ is read as "is distributed as." The letter $X$ stands for the thing you are counting or measuring. Binomial: $X \sim \text{Bin}(n, p)$ "X is distributed binomial with $n$ trials and success probability $p$." Poisson: $X \sim \text{Pois}(\lambda)$ Read: "X is distributed Poisson with rate $\lambda$." Normal: $X \sim N(\mu, \sigma^2)$ Read: "X is distributed normal with mean $\mu$ and variance $\sigma^2$. | Distribution | Parameters | Meaning | |--------------|-----------------|------------------------------------------| | Binomial | $n$, $p$ | number of trials, probability of success | | Poisson | $\lambda$ | average number of events per interval | | Normal | $\mu$, $\sigma$ | mean, standard deviation | Once we identify the parameters of interest, we can use R to make our lives easier when using these distributions ## How R names these functions R uses a naming system: a prefix describing what you want, plus a root naming the distribution. The roots: | Distribution | Root | |--------------|-------| | Binomial | binom | | Poisson | pois | | Normal | norm | The prefixes: | Prefix | What it gives you | |--------|-------------------------------------------------------------| | d | the probability of exactly one specific value (or density for continuous random variables) | | p | the probability of that value or anything smaller | | q | works backwards: you give a probability, it returns a value | | r | random values drawn from the distribution | Combine the prefix and distribution to get functions: | | Binomial | Poisson | Normal | |-----|----------|---------|--------| | d | dbinom | dpois | dnorm | | p | pbinom | ppois | pnorm | | q | qbinom | qpois | qnorm | | r | rbinom | rpois | rnorm | ------------------------------------------------------------------------ ## The Binomial distribution A quiz has 12 multiple-choice questions, each with 4 options. A student guesses randomly on every question. $$X \sim \text{Bin}(12, 0.25)$$ ```{r} n <- 12 p <- 0.25 ``` ### dbinom - exactly one value Question: What is the probability the student gets exactly 5 correct? In symbols: $P(X = 5)$ ```{r} dbinom(5, size = n, prob = p) ``` There is about a 10.3% chance of getting exactly 5 correct. Note: R uses "size" and "prob" arguments rather than "n" and "p" You can ask for several values at once. Giving 0:12 returns the probability of every possible outcome. This gives us the probability distribution ```{r} dbinom(0:12, size = n, prob = p) ``` ### pbinom - a value or anything smaller Question: What is the probability the student gets 3 or fewer correct? In symbols: $P(X \leq 3)$ ```{r} pbinom(3, size = n, prob = p) ``` This will yield the same result: ```{r} sum(dbinom(0:3, size = n, prob = p)) ``` ### Going the other direction Question: What is the probability of getting at least 6 correct? ```{r} 1 - pbinom(5, size = n, prob = p) ``` R has a shortcut for this. Adding lower.tail = FALSE as an argument flips the direction. NOTE: When lower.tail = FALSE is used, R calculates the probability of values greater than the number specified. It does not include the specified number. ```{r} pbinom(5, size = n, prob = p, lower.tail = FALSE) ``` This will calculate the probability getting 6 or more questions correct. Alternatively, you can take the sum of probabilities over the specified interval. ```{r} sum(dbinom(6:12, size = n, prob = p)) ``` ### Seeing the distribution Plotting dbinom for every outcome shows the shape ```{r} binom_df <- data.frame(x = 0:12) binom_df$prob <- dbinom(binom_df$x, size = n, prob = p) ggplot(binom_df, aes(x = x, y = prob)) + geom_col(fill = "lightblue") + labs( x = "Number correct", y = "P(X = x)") ``` ### qbinom and rbinom qbinom runs backwards. Give it a probability and it returns the value ```{r} qbinom(0.90, size = n, prob = p) ``` That says 90% of guessing students score 5 or fewer. rbinom simulates. Here are 1000 imaginary students taking the quiz ```{r} #set.seed(90210) quizzes <- data.frame(correct = rbinom(1000, size = n, prob = p)) ggplot(quizzes, aes(x = correct)) + geom_bar(fill = "lightblue") + labs(x = "Number correct", y = "Number of students") ``` ## The Poisson distribution The parameter, $\lambda$ (lambda), the average number of events per interval. > A campus help line receives an average of 4 calls per hour. $$X \sim \text{Pois}(4)$$ Note: lambda = 4 is the expected number of calls in ONE hour. If you want the number of calls in a workday (8 hours), you must multiply by 8 to get that distribution: lambda = 32. ```{r} lambda <- 4 ``` ### dpois - exactly one value Question: What is the probability of exactly 3 calls in an hour? In symbols: $P(X = 3)$ ```{r} dpois(3, lambda = lambda) ``` About a 19.5% chance of exactly 3 calls ### ppois - a value or anything smaller Question: What is the probability of 2 or fewer calls? In symbols: $P(X \leq 2)$ ```{r} ppois(2, lambda = lambda) ``` Question: What is the probability of more than 6 calls? ```{r} ppois(6, lambda = lambda, lower.tail = FALSE) ``` ### Seeing the distribution ```{r} pois_df <- data.frame(k = 0:15) pois_df$prob <- dpois(pois_df$k, lambda = lambda) ggplot(pois_df, aes(x = k, y = prob)) + geom_col(fill = "darkorange") + labs(x = "Number of calls",y = "P(X = k)") ``` ### qpois and rpois ```{r} qpois(0.95, lambda = lambda) set.seed(801) calls <- rpois(1000, lambda = lambda) ``` ------------------------------------------------------------------------ ## The Normal distribution The normal takes two parameters, the mean $\mu$ and the variance $\sigma^2$. In R these are the arguments mean and sd. Note: sd is the standard deviation, not the variance. If a problem tells you the variance is 25, you must take the square root and pass sd = 5 ### What changes for a continuous distribution Because a measurement can land on any value, the probability of hitting one exact number is zero. $P(X = 70)$ is 0 Two consequences: - Every normal question is about a range, never a single value. - dnorm is not a probability. It's only the height of the curve, useful for drawing > Adult male heights are approximately normal with a mean of 70 inches and a standard deviation of 3 inches. $$X \sim N(70, 9)$$ ```{r} mu <- 70 sigma <- 3 ``` ### pnorm - the area to the left Question: What proportion of men are shorter than 66 inches? In symbols: $P(X < 66)$ ```{r} pnorm(66, mean = mu, sd = sigma) ``` Answer: About 9% of men are shorter than 66 inches. Question: What proportion are taller than 74 inches? ```{r} pnorm(74, mean = mu, sd = sigma, lower.tail = FALSE) ``` Question: What proportion are between 66 and 74 inches? Take everything below 74 and subtract off everything below 66. What remains is everything between 74 and 66 ```{r} pnorm(74, mean = mu, sd = sigma) - pnorm(66, mean = mu, sd = sigma) ``` ### Seeing the distribution ```{r} curve_df <- data.frame(x = seq(58, 82, length.out = 1000)) curve_df$density <- dnorm(curve_df$x, mean = mu, sd = sigma) ggplot(curve_df, aes(x = x, y = density)) + geom_line(linewidth=1) + geom_area(data = subset(curve_df, x <= 66), fill = "lightblue") + labs(x = "Height (inches)",y = "Density") ``` ### qnorm - going backwards from a probability Question: How tall is a man at the 90th percentile? ```{r} qnorm(0.90, mean = mu, sd = sigma) ``` Answer: A man at the 90th percentile is about 73.8 inches tall. ### rnorm - simulation ```{r} heights <- rnorm(1000, mean = mu, sd = sigma) mean(heights) sd(heights) ``` The mean and sd of the simulated normal distribution are very close to the true parameters # Practice Problems Answer each question in the code chunk provided. Where a problem asks you to state a distribution, write it in LaTeX using the notation from the lab. ## Problem 1: > A seed company claims 85% of its seeds germinate. A gardener plants 20 seeds. Let $X$ be the number that germinate. (a) State the distribution of $X$. $$X \sim$$ (b) What is the probability that exactly 18 seeds germinate? ```{r} ``` (c) What is the probability that at least 18 germinate? ```{r} ``` (d) What is the probability that 15 or fewer germinate? ```{r} ``` (e) What is the probability that between 16 and 19 germinate? ```{r} ``` (f) Use ggplot2 to make a bar plot of the distribution. ```{r} ``` ## Problem 2: > A busy intersection averages 3.2 accidents per month. (a) State the distribution of the monthly accident count $X$ $$X \sim$$ (b) What is the probability of exactly 5 accidents in a month? ```{r} ``` (c) What is the probability of no accidents in a month? ```{r} ``` (d) What is the probability of at least 4 accidents in a month? ```{r} ``` (e) What is the probability of more than 40 accidents in a year? Remember to rescale $\lambda$ ```{r} ``` (f) The city wants enough emergency response capacity to handle the monthly accident count in 99% of months. What number should they plan for? (Hint: you are finding a value, not a probability) ```{r} ``` (g) Use ggplot2 to make a plot of the distribution ```{r} ``` ## Problem 3: > A manufacturer's batteries last an average of 500 hours with a standard deviation of 45 hours, and battery life is approximately normally distributed. (a) State the distribution of battery life $X$. $$X \sim$$ (b) What is the probability a battery lasts less than 425 hours? ```{r} ``` (c) What is the probability a battery lasts more than 560 hours? ```{r} ``` (d) What proportion of batteries last between 450 and 550 hours? ```{r} ``` (e) The company will replace the shortest-lasting 2% of batteries under warranty. What lifetime should the warranty cover? ```{r} ``` (f) Use ggplot2 to plot the distribution of battery life. (Hint: build a data frame of x values from 350 to 650, use dnorm for the curve height, and draw it with geom_line.) ```{r} ``` ## Problem 4: Choosing the right distribution For each scenario, name the distribution and compute the requested probability. (a) A basketball player makes 78% of her free throws. She shoots 10 in a game. What is the probability she makes exactly 9? ```{r} ``` (b) A website receives an average of 12 visits per minute. What is the probability it receives fewer than 8 visits in a given minute? ```{r} ``` (c) Scores on a standardized exam are normally distributed with a mean of 1050 and a variance of 40000. What score is at the 75th percentile? ```{r} ``` # Final Step Render your document. Click the Render button at the top of the editor, or press Ctrl + Shift + K. If the render fails, read the error message. It names the chunk that caused the problem. The most common causes are a missing closing parenthesis, or an object was used before it was created.