Wednesday 2 December 2015

Coin-tossing power

I've been doing some coin tossing. Well actually it's cheminformatics, but the problem reduces to coin tossing. Given that I toss a coin 1000 times, how many heads must I observe to believe that it is a biased coin. My usual ramshackle approach would be to estimate the standard deviation of the random distribution (have my computer do some coin tossing) and then say something about being two sigmas away from the mean. I've done that just to be sure - the sigma is just under 16.
import random
import matplotlib.pyplot as plt
from collections import defaultdict
import scipy
import scipy.optimize
import numpy as np

values = [01]

ans = defaultdict(int)
for N in range(100000):
    tot = 0
    for i in range(1000):
        tot += random.choice(values)
    ans[tot] += 1

start, end = 350650
x = np.arange(start, end)
y = []
for i in range(start, end):
    if i in ans:
        if i > start:

n = len(x)
mean = 500.
sigma = 10.

def gaus(x,a,sigma):
    return a*scipy.exp(-(x-mean)**2/(2*sigma**2))

popt,pcov = scipy.optimize.curve_fit(gaus,x,y,p0=[1.0,sigma])
print popt

PMC points out that a slightly easier way of getting the same value would be to use an equation: variance = n(1-p)p where n = 1000 and p is 0.5. The standard deviation is then the square root of this (i.e. sqrt of 250), 15.8.

However, the proper way of handling the original question is a power calculation. Typically power calculations are associated with calculating the necessary sample size. Here I have a fixed sample size (n=1000) and I want to figure out, given that the alternative hypothesis is true (biased coin), what number of heads must I observe to be 99.9% sure (power=0.999) that it would be show up as significant at the 0.1% level (alpha=0.001). The y = 0.5 below refers to the proportion of heads expected under the null hypothesis (unbiased coin). Since n=1000, we can use the normal approximation to the binomial distribution.
import math
import scipy.stats

def qnorm(p):
    return scipy.stats.norm.ppf(p)

def solvequadratic(a, b, c):
    return [(-b+math.sqrt((b**2)-(4*(a*c))))/(2.*a),

if __name__ == "__main__":
    alpha = 0.001 # Significance level
    gamma = 0.999 # Power
    qgamma = qnorm(gamma)
    qalpha = qnorm(1.-(alpha/2.))
    p = (qalpha+qgamma)**2
    n = 1000
    y = 0.5
    a = 2*n+p
    b = (2*p-4*n)*y - 2*p
    # Note that if y is 0.5, then, b = -2*n-p (i.e. -a)
    c = -2*p*y + (2*n+p)*y*y
    print solvequadratic(a, b, c)
...and the answer? 642. Thanks to ALC for help with this, though all errors are my own.

Notes: (added 04/12/2015)
Both the power and the significance level are conditional probabilities:
  • The significance level (alpha) is the probability of rejecting the null hypothesis given that it is true, ie. prob(rejecting null hypothesis | null hypothesis is correct).
  • The power (gamma) is the probability of detecting a difference, if indeed the difference does exist, ie. prob(rejecting null hypothesis | null hypothesis is incorrect).