---
title: "IPS9 in R: Multiple regression (Chapter 11)"
author: "Nicholas Horton (nhorton@amherst.edu)"
date: "January 19, 2019"
output: 
  pdf_document:
    fig_height: 3
    fig_width: 5
  html_document:
    fig_height: 3
    fig_width: 5
  word_document:
    fig_height: 4
    fig_width: 6
---


```{r, include = FALSE}
# Don't delete this chunk if you are using the mosaic package
# This loads the mosaic and dplyr packages
require(mosaic)
```

```{r, include = FALSE}
# knitr settings to control how R chunks work.
knitr::opts_chunk$set(
  tidy = FALSE,     # display code as typed
  size = "small"    # slightly smaller font for code
)
```

## Introduction and background 

These documents are intended to help describe how to undertake analyses introduced 
as examples in the Ninth Edition of \emph{Introduction to the Practice of Statistics} (2017) by Moore, McCabe, and Craig.

More information about the book can be found [here](https://macmillanlearning.com/Catalog/product/introductiontothepracticeofstatistics-ninthedition-moore).
The data used in these documents can be found under Data Sets in the [Student Site](https://www.macmillanlearning.com/catalog/studentresources/ips9e?_ga=2.29224888.526668012.1531487989-1209447309.1529940008#). This
file as well as the associated R Markdown reproducible analysis source file used to create it can be found at https://nhorton.people.amherst.edu/ips9/.

This work leverages initiatives undertaken by Project MOSAIC (http://www.mosaic-web.org), an NSF-funded effort to improve the teaching of statistics, calculus, science and computing in the undergraduate curriculum. In particular, we utilize the `mosaic` package, which was written to simplify the use of R for introductory statistics courses. A short summary of the R needed to teach introductory statistics can be found in the mosaic package vignettes (http://cran.r-project.org/web/packages/mosaic).  A paper describing the mosaic approach was published in the *R Journal*: https://journal.r-project.org/archive/2017/RJ-2017-024.
  
## Chapter 11: Multiple Regression
This file replicates the analyses from Chapter 11: Multiple Regression.

First, load the packages that will be needed for this document: 

```{r load-packages}
library(mosaic)
library(readr)
```

### Section 11.1: Inference for multiple regression

#### Example 11.1: Predicting early success in college

```{r eg11-1, message=FALSE}
GPA <- read_csv("https://nhorton.people.amherst.edu/ips9/data/chapter11/EG11-01GPA.csv")
# Figure 11.1, page 609
head(GPA)
```

### Section 11.2: A Case Study

```{r}
# Figure 11.2, page 619
favstats(~ GPA, data = GPA)
favstats(~ HSM, data = GPA)
favstats(~ HSS, data = GPA)
favstats(~ HSE, data = GPA)
favstats(~ SATM, data = GPA)
favstats(~ SATCR, data = GPA)
favstats(~ SATW, data = GPA)
```

```{r}
# Figure 11.3, page 620
gf_histogram(~ HSM, data = GPA) %>%
  gf_labs(y = "Percent")# Doesn't look great
gf_histogram(~ HSS, data = GPA) %>%
  gf_labs(y = "Percent")
gf_histogram(~ HSE, data = GPA) %>%
  gf_labs(y = "Percent")
```

#### Relationships between pairs of variables

```{r}
# Figure 11.4, page 621
options(digits = 2)
cor(GPA)
```

#### Example 11.13: Pairwise relationships among variables in the GPA data set

```{r message = FALSE, fig.width = 7, fig.height = 8}
GPA <- read_csv("https://nhorton.people.amherst.edu/ips9/data/chapter11/EX11-13GPA.csv")
GPA <- GPA %>%
  mutate(SEX = ifelse(SEX == 1, "F", "M"))
library(GGally)
# Figure 11.5
GPA %>% select(-OBS) %>%
  GGally::ggpairs()
```

#### Regression on high school grades

```{r}
# Figure 11.6, page 623
gpamultlm <- lm(GPA ~ HSM + HSE + HSS, data = GPA)
msummary(gpamultlm)
```

#### Examining the residuals

```{r}
# Figure 11.7, page 625
gf_qq(~ resid(gpamultlm)) %>% 
  gf_labs( x = "Normal Score", y = "Residual")
gf_histogram(~ resid(gpamultlm), binwidth = .5) %>%
  gf_labs(x = "Residual", y = "Percent")
```

#### Example 11.14: Residual plots for the GPA analysis

#### Refining the model

```{r}
# Figure 11.8, page 626
gpamultlm2 <- lm(GPA ~ HSM + HSS, data = GPA)
msummary(gpamultlm2)
```

#### Regression using all variables

```{r}
# Figure 11.9
gpasatlm <- lm(GPA ~ SATM + SATCR + SATW, data = GPA)
msummary(gpasatlm)

# Figure 11.10, page 628
gpaalllm <- lm(GPA ~ SATM + SATCR + SATW + HSS + HSE + HSM, data = GPA)
msummary(gpaalllm)

# Figure 11.11, page 631
MASS::stepAIC(gpaalllm) 
```