Chi-sqaure test in Python

Question

I want to perform a Chi-square test on a known sample in Python. Since I come from R, to my knowledge I can do something like this:

x.poi<-rpois(n=200,lambda=2.5)
gf <-goodfit(x.poi,type= "poisson",method= "MinChisq")
summary(gf)

and then I can just call the summary function and get my results.

I know that in Python scipy provides a chi-square test, however, it is needed to provide an expected array of samples.

Is there an equivalent version of this R function for Python?

score 1 · Answer 1 · answered May 06 '20 at 20:22

You cannot get exactly the same, without implementing an optimization for the MinChisq estimate of the mean of your poisson, $\hat{\lambda}$.

So below is an example using the "ML" option to estimate $\hat{\lambda}$, and you still get a chi-sq test in the end. This is convenient because the MLE estimator of lambda will be the mean:

set.seed(111)
x.poi<-rpois(n=200,lambda=2.5)
gf = goodfit(x.poi,type= "poisson",method= "ML")
summary(gf)

     Goodness-of-fit test for poisson distribution

                      X^2 df  P(> X^2)
Likelihood Ratio 6.874807  7 0.4420304

gf$par
$lambda
[1] 2.545

mean(x.poi)
[1] 2.545

write.csv(x.poi,"x.poi.csv")

We calculate the expected using the mean as $\hat{\lambda}$ :

import pandas as pd
import numpy as np
import scipy 

x_poi = pd.read_csv("x.poi.csv")['x']
obs = np.bincount(x_poi)
Lambda = x_poi.mean()
expected = scipy.stats.poisson.pmf(np.arange(len(obs)),Lambda)*len(x_poi)

You need to use the G-test and not the pearson chi-square, so in python it will be:

scipy.stats.power_divergence(obs,expected,lambda_="log-likelihood".,ddof=1)
[Power_divergenceResult(statistic=6.874807063434596, pvalue=0.44203040359775747)

Chi-sqaure test in Python

1 Answers1