T-test in Pandas

If I want to calculate the mean of two categories in Pandas, I can do it like this:

data = {'Category': ['cat2','cat1','cat2','cat1','cat2','cat1','cat2','cat1','cat1','cat1','cat2'], 'values': [1,2,3,1,2,3,1,2,3,5,1]}
my_data = DataFrame(data)
my_data.groupby('Category').mean()
Category: values:
cat1 2.666667
cat2 1.600000

I have a lot of data formatted this way, and now I need to do a T-test to see if the mean of cat1 and cat2 are statistically different. How can I do that?

3 Answers

it depends what sort of t-test you want to do (one sided or two sided dependent or independent) but it should be as simple as:

from scipy.stats import ttest_ind
cat1 = my_data[my_data['Category']=='cat1']
cat2 = my_data[my_data['Category']=='cat2']
ttest_ind(cat1['values'], cat2['values'])
>>> (1.4927289925706944, 0.16970867501294376)

it returns a tuple with the t-statistic & the p-value

see here for other t-tests

EDIT: I had not realized this was about the data format. You could use

import pandas as pd
import scipy
two_data = pd.DataFrame(data, index=data['Category'])

Then accessing the categories is as simple as

scipy.stats.ttest_ind(two_data.loc['cat'], two_data.loc['cat2'], equal_var=False)

The loc operator accesses rows by label.

As @G Garcia said

one sided or two sided dependent or independent

If you have two independent samples but you do not know that they have equal variance, you can use Welch's t-test. It is as simple as

scipy.stats.ttest_ind(cat1['values'], cat2['values'], equal_var=False)

For reasons to prefer Welch's test, see .

For two dependent samples, you can use

scipy.stats.ttest_rel(cat1['values'], cat2['values'])

I simplify the code a little bit.

from scipy.stats import ttest_ind
ttest_ind(*my_data.groupby('Category')['value'].apply(lambda x:list(x)))