welford 0.2.5

Python (numpy) implementation of Welford's algorithm.

Python (Numpy) implementation of Welford’s algorithm, which is online or parallel algorithm for calculating variances.

The algorithm is described in the followings,

• Wikipedia:Welford Online Algorithm

• Wikipedia:Welford Parallel Algorithm

Welford’s method is more numerically stable than the standard method. The theoritical background of Welford’s method is mentioned in detail on the following blog articles. Please refer them if you are interested in.

• http://www.johndcook.com/blog/standard_deviation

• https://jonisalonen.com/2013/deriving-welfords-method-for-computing-variance/

This library is inspired by the jvf’s implementation, which is implemented without using numpy library.

Install

Download package via PyPI repository

$ pip install welford

Example

For Online Calculation

import numpy as np
from welford import Welford

# Initialize Welford object
w = Welford()

# Input data samples sequentialy
w.add(np.array([0, 100]))
w.add(np.array([1, 110]))
w.add(np.array([2, 120]))

# output
print(w.mean)  # mean --> [  1. 110.]
print(w.var_s)  # sample variance --> [1, 100]
print(w.var_p)  # population variance --> [ 0.6666 66.66]

# You can add other samples after calculating variances.
w.add(np.array([3, 130]))
w.add(np.array([4, 140]))

# output with added samples
print(w.mean)  # mean --> [  2. 120.]
print(w.var_s)  # sample variance --> [  2.5 250. ]
print(w.var_p)  # population variance --> [  2. 200.]

Welford object supports initialization with data samples and batch addition of samples.

# Initialize Welford object with samples
ini = np.array([[0, 100],
                [1, 110],
                [2, 120]])
w = Welford(ini)

# output
print(w.mean)  # mean --> [  1. 110.]
print(w.var_s)  # sample variance --> [1, 100]
print(w.var_p)  # population variance --> [ 0.66666667 66.66666667]

# add other samples through batch method
other_samples = np.array([[3, 130],
                          [4, 140]])
w.add_all(other_samples)

# output with added samples
print(w.mean)  # mean --> [  2. 120.]
print(w.var_s)  # sample variance --> [  2.5 250. ]
print(w.var_p)  # population variance --> [  2. 200.]

For Parallel Calculation

Welford also offers parallel calculation method for variance.

import numpy as np
from welford import Welford

# Initialize two Welford objects
w_1 = Welford()
w_2 = Welford()

# Each object will calculate variance of each samples in parallel.
# On w_1
w_1.add(np.array([0, 100]))
w_1.add(np.array([1, 110]))
w_1.add(np.array([2, 120]))
print(w_1.var_s)  # sample variance -->[  1. 100.]
print(w_1.var_p)  # population variance -->[ 0.66666667 66.66666667]

# On w_2
w_2.add(np.array([3, 130]))
w_2.add(np.array([4, 140]))
print(w_2.var_s)  # sample variance -->[ 0.5 50. ]
print(w_2.var_p)  # sample variance -->[ 0.25 25.  ]

# You can Merge objects to get variance of WHOLE samples
w_1.merge(w_2)
print(w.var_s)  # sample variance --> [  2.5 250. ]
print(w_1.var_p)  # sample variance -->[  2. 200.]