# Set up packages for lecture. Don't worry about understanding this code, but
# make sure to run it if you're following along.
import numpy as np
import babypandas as bpd
import pandas as pd
from matplotlib_inline.backend_inline import set_matplotlib_formats
import matplotlib.pyplot as plt
from scipy import stats
set_matplotlib_formats("svg")
plt.style.use('ggplot')

np.set_printoptions(threshold=20, precision=2, suppress=True)
pd.set_option("display.max_rows", 7)
pd.set_option("display.max_columns", 8)
pd.set_option("display.precision", 2)

from ipywidgets import widgets
from IPython.display import clear_output, display

import warnings
warnings.filterwarnings('ignore')

def standard_units(any_numbers):
    "Convert a sequence of numbers to standard units."
    return (any_numbers - any_numbers.mean()) / np.std(any_numbers)

def standardize(df):
    """Return a DataFrame in which all columns of df are converted to standard units."""
    df_su = bpd.DataFrame()
    for column in df.columns:
        df_su = df_su.assign(**{column + ' (su)': standard_units(df.get(column))})
    return df_su

def correlation(df, x, y):
    '''Computes the correlation between column x and column y of df.'''
    return (standard_units(df.get(x)) * standard_units(df.get(y))).mean()

def slope(df, x, y):
    '''Returns the slope of the regression line between columns x and y in df (in original units).'''
    r = correlation(df, x, y)
    return r * np.std(df.get(y)) / np.std(df.get(x))

def intercept(df, x, y):
    '''Returns the intercept of the regression line between columns x and y in df (in original units).'''
    return df.get(y).mean() - slope(df, x, y) * df.get(x).mean()

# All of the following code is for visualization.
def plot_regression_line(df, x, y, margin=.02, alpha=1):
    '''Computes the slope and intercept of the regression line between columns x and y in df (in original units) and plots it.'''
    m = slope(df, x, y)
    b = intercept(df, x, y)
    
    df.plot(kind='scatter', x=x, y=y, s=50, figsize=(10, 5), label='original data', alpha=alpha)
    left = df.get(x).min()*(1 - margin)
    right = df.get(x).max()*(1 + margin)
    domain = np.linspace(left, right, 10)
    plt.plot(domain, m*domain + b, color='orange', label='regression line', lw=4)
    plt.suptitle(format_equation(m, b), fontsize=18)
    plt.legend();

def format_equation(m, b):
    if b > 0:
        return r'$y = %.2fx + %.2f$' % (m, b)
    elif b == 0:
        return r'$y = %.2fx' % m
    else:
        return r'$y = %.2fx %.2f$' % (m, b)

Lecture 25 – Residuals and Inference

DSC 10, Winter 2023

Announcements

• The Final Project is due tomorrow at 11:59PM.
  • You can use slip days if needed.
  • If one or both partners has run out of slip days and you submit the project late, we will reallocate slip days towards the final project, away from lesser-weighted assignments. See the syllabus.
• The Final Exam is this Saturday 3/18 from 3PM to 6PM.
  • More details coming shortly, but start studying!
• Today is the last day of new material. The next two days are for review!

Agenda

• Residuals.
• Inference for regression.

Residuals

Quality of fit

• The regression line describes the "best linear fit" for a given dataset.
• The formulas for the slope and intercept work no matter what the shape of the data is.
• However, the line is only meaningful if the relationship between $x$ and $y$ is roughly linear.

Example: Non-linear data

np.random.seed(23)
x2 = bpd.DataFrame().assign(
    x=np.arange(-6, 6.1, 0.5) + np.random.normal(size=25), 
    y=np.arange(-6, 6.1, 0.5)**2 + np.random.normal(size=25)
)
plot_regression_line(x2, 'x', 'y')

This line doesn't fit the data at all, despite being the "best" line for the data!

Residuals

• Any set of predictions has errors.

$$\text{error} = \text{actual } y - \text{predicted } y$$

• When using the regression line to make predictions, the errors are called residuals.

$$\text{residual} = \text{actual } y - \text{predicted } y \text{ by regression line}$$

• There is one residual corresponding to each data point $(x, y)$ in the dataset.

Calculating residuals

def predicted(df, x, y):
    m = slope(df, x, y)
    b = intercept(df, x, y)
    return m * df.get(x) + b

def residual(df, x, y):
    return df.get(y) - predicted(df, x, y)

Example: Predicting a son's height from his mother's height 👵👨 📏

Is the association between 'mom' and 'son' linear?

• If there is a linear association, is it strong?
  • We can answer this using the correlation coefficient.
  • Close to 0 = weak, close to -1/+1 = strong.

• Is "linear" the best description of the association between 'mom' and 'son'?
  • We'll use residuals to answer this question.

galton = bpd.read_csv('data/galton.csv')

male_children = galton[galton.get('gender') == 'male']
mom_son = bpd.DataFrame().assign(mom = male_children.get('mother'), 
                                 son = male_children.get('childHeight'))

mom_son_predictions = mom_son.assign(
    predicted=predicted(mom_son, 'mom', 'son'),
    residuals=residual(mom_son, 'mom', 'son'),
)

plot_regression_line(mom_son_predictions, 'mom', 'son')

idx = np.random.randint(0, mom_son_predictions.shape[0], size=50)
for i, k in enumerate(idx):
    x = mom_son_predictions.get('mom').iloc[k]
    y = mom_son_predictions.get('son').iloc[k]
    p = mom_son_predictions.get('predicted').iloc[k]
    plt.plot([x,x], [y,p], linewidth=3, color='purple', label='residuals' if i==0 else None)
plt.legend();
print('Correlation:', correlation(mom_son, 'mom', 'son'))

Correlation: 0.32300498368490554

Residual plots

• The residual plot of a regression line is the scatter plot with the $x$ variable on the $x$-axis and residuals on the $y$-axis.

  $$\text{residual} = \text{actual } y - \text{predicted } y \text{ by regression line}$$

• Residual plots describe how the error in the regression line's predictions varies.

• Key idea: If a linear fit is good, the residual plot should look like a patternless "cloud" ☁️.

mom_son_predictions.plot(kind='scatter', x='mom', y='residuals', s=50, c='purple', figsize=(10, 5), label='residuals')
plt.axhline(0, linewidth=3, color='k', label='y = 0')
plt.title('Residual plot for predicting son\'s height based on mother\'s height')
plt.legend();

The residual plot for a non-linear association 🚗

• Consider the hybrid cars dataset from earlier.
• Let's look at a regression line that uses 'mpg' to predict 'price'.

hybrid = bpd.read_csv('data/hybrid.csv')
mpg_price = hybrid.assign(
    predicted=predicted(hybrid, 'mpg', 'price'),
    residuals=residual(hybrid, 'mpg', 'price')
)
mpg_price

	vehicle	year	price	acceleration	mpg	class	predicted	residuals
0	Prius (1st Gen)	1997	24509.74	7.46	41.26	Compact	32609.64	-8099.90
1	Tino	2000	35354.97	8.20	54.10	Compact	19278.39	16076.58
2	Prius (2nd Gen)	2000	26832.25	7.97	45.23	Compact	28487.75	-1655.50
...	...	...	...	...	...	...	...	...
150	C-Max Energi Plug-in	2013	32950.00	11.76	43.00	Midsize	30803.06	2146.94
151	Fusion Energi Plug-in	2013	38700.00	11.76	43.00	Midsize	30803.06	7896.94
152	Chevrolet Volt	2013	39145.00	11.11	37.00	Compact	37032.62	2112.38

153 rows × 8 columns

# Plot of the original data and regression line.
plot_regression_line(hybrid, 'mpg', 'price');
print('Correlation:', correlation(hybrid, 'mpg', 'price'))

Correlation: -0.5318263633683789

# Residual plot.
mpg_price.plot(kind='scatter', x='mpg', y='residuals', figsize=(10, 5), s=50, color='purple', label='residuals')
plt.axhline(0, linewidth=3, color='k', label='y = 0')
plt.title('Residual plot for regression between mpg and price')
plt.legend();

Note that as 'mpg' increases, the residuals go from being mostly large, to being mostly small, to being mostly large again. That's a pattern!

Issue: Patterns in the residual plot

• Patterns in the residual plot imply that the relationship between $x$ and $y$ may not be linear.
  • While this can be spotted in the original scatter plot, it may be easier to identify in the residual plot.

• In such cases, a curve may be a better choice than a line for prediction.
  • In future courses, you'll learn how to extend linear regression to work for polynomials and other types of mathematical functions.

Another example: 'mpg' and 'acceleration' ⛽

• Let's fit a regression line that predicts 'mpg' given 'acceleration'.
• Let's then look at the resulting residual plot.

accel_mpg = hybrid.assign(
    predicted=predicted(hybrid, 'acceleration', 'mpg'),
    residuals=residual(hybrid, 'acceleration', 'mpg')
)
accel_mpg

	vehicle	year	price	acceleration	mpg	class	predicted	residuals
0	Prius (1st Gen)	1997	24509.74	7.46	41.26	Compact	43.29	-2.03
1	Tino	2000	35354.97	8.20	54.10	Compact	41.90	12.20
2	Prius (2nd Gen)	2000	26832.25	7.97	45.23	Compact	42.33	2.90
...	...	...	...	...	...	...	...	...
150	C-Max Energi Plug-in	2013	32950.00	11.76	43.00	Midsize	35.17	7.83
151	Fusion Energi Plug-in	2013	38700.00	11.76	43.00	Midsize	35.17	7.83
152	Chevrolet Volt	2013	39145.00	11.11	37.00	Compact	36.40	0.60

153 rows × 8 columns

# Plot of the original data and regression line.
plot_regression_line(accel_mpg, 'acceleration', 'mpg')
print('Correlation:', correlation(accel_mpg, 'acceleration', 'mpg'))

Correlation: -0.5060703843771185

# Residual plot.
accel_mpg.plot(kind='scatter', x='acceleration', y='residuals', figsize=(10, 5), s=50, color='purple', label='residuals')
plt.axhline(0, linewidth=3, color='k', label='y = 0')
plt.title('Residual plot for regression between acceleration and price')
plt.legend();