Constructing a co-occurrence matrix in python pandas

Question

I know how to do this in R. But, is there any function in pandas that transforms a dataframe to an nxn co-occurrence matrix containing the counts of two aspects co-occurring

Answer 1

It's a simple linear algebra, you multiply matrix with its transpose (your example contains strings, don't forget to convert them to integer):

>>> df_asint = df.astype(int)
>>> coocc = df_asint.T.dot(df_asint)
>>> coocc
       Dop  Snack  Trans
Dop      4      2      3
Snack    2      3      2
Trans    3      2      4

if, as in R answer, you want to reset diagonal, you can use numpy's fill_diagonal:

>>> import numpy as np
>>> np.fill_diagonal(coocc.values, 0)
>>> coocc
       Dop  Snack  Trans
Dop      0      2      3
Snack    2      0      2
Trans    3      2      0