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Linear Regression using Scipy

There are many approaches to perform linear regression (or least squares fit) in Python and libraries which support doing so. One approach I have come across, which I personally find advantegous, provide additional variables compared to other solutions. This post hereby intends to explain, through a simple example, how to utilize the library and the additional variables hereof.

Implementing Linear Regression

To perform linear regression, we will utilize both scipy and numpy as the two provide numerous advantages when used together. If in doubt, refer to the litterature at the end of the post to find the definition of a specific term.

Likewise, when the two libraries are combined, they additionally solve an issue when calculating the traversing line: if the slope of the line became less than zero, a calculation error occured.

The implementation, which can also be found on Github, is as follows:

# -*- coding: utf-8 -*-

Created on 10th of March, 2014

@author: David K. Laundav

from scipy import stats
from numpy import arange, poly1d, random
import matplotlib.pyplot as plt
from math import sqrt

# ----------------------------------
# Notes:
#     This is only example data, and should be substitued with your own
x = arange(0,9) 
y = [int(20*random.random()) for i in range(len(x))]

# ----------------------------------
# Notes:
#     alpha = the slope of the curve
#     beta = the point at which the slope intercepts at x = 0
#     r_value = the correlation coefficient
#     p_value = the p-value which the h0 hypothesis is tested against
#         In this case, a p-value of 0.0 would be a 100% match, indicating that the linear regression is perfectly aligned with the data points
#     std_err = the standard deviation
alpha, beta, r_value, p_value, std_err = stats.linregress(x, y) # Use scipy to calculate the variables of the least squares fit
polynomial = poly1d([alpha, beta]) # Calculate the polynomial least squares fit as: "y = ax * b"
line = polynomial(x) # Returns an array containing the carry sum of "beta -/+ alpha" for each element in x (+ if the slope is positive, otherwise -)
sose = sqrt(sum((line-y)**2)/len(y)) # Calculate the Sum of Squared Errors

fig = plt.figure()
ax = fig.add_subplot(111)

""" Writing the variables to the plot """
text_string = "Alpha: %f" % (alpha)
text_string += "\nBeta: %f" % (beta)
text_string += "\nCorrelation coefficient: %f" % (r_value)
text_string += "\nP-value: %f" % (p_value)
text_string += "\nStandard deviation: %f" % (std_err)
text_string += "\nSum of squared error: %f" % (sose)
ax.text(0.022, 0.972, text_string, transform=ax.transAxes, verticalalignment='top', bbox=dict(facecolor='none', pad=10), fontsize=8)

""" Plotting the data """
ax.scatter(0, beta, color='red', label='Intercept')
ax.scatter(x, y, color='grey', label='Data')
ax.plot(line, color='blue', label='Linear Regression')
ax.legend(loc=1, fontsize=10)


Linear Regression using Scipy and Numpy with a positive slope where y = [5, 2, 2, 8, 6, 12, 14, 5, 10]

Linear Regression using Scipy and Numpy with an upwards slope where y = [5, 2, 2, 8, 6, 12, 14, 5, 10]

Linear Regression using Scipy and Numpy with a downwards slope where [15, 12, 12, 8, 9, 14, 10, 5, 9]

Linear Regression using Scipy and Numpy with a downwards slope where y = [15, 12, 12, 8, 9, 14, 10, 5, 9]


Now, you may not be familiar with either correlation coefficients, p-valuesstandard devitiation or the sum of squared errors. Fortunately, much literature already exist in this matter:


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