def _G_test(site_counts):
"""G test for 2x2 contingency table (PRIVATE).
Argument:
- site_counts - [syn_fix, nonsyn_fix, syn_poly, nonsyn_poly]
>>> print("%0.6f" % _G_test([17, 7, 42, 2]))
0.004924
"""
# TODO:
# Apply continuity correction for Chi-square test.
from math import log
# from scipy.stats import chi2
G = 0
tot = sum(site_counts)
tot_syn = site_counts[0] + site_counts[2]
tot_non = site_counts[1] + site_counts[3]
tot_fix = sum(site_counts[:2])
tot_poly = sum(site_counts[2:])
exp = [
tot_fix * tot_syn / tot, tot_fix * tot_non / tot,
tot_poly * tot_syn / tot, tot_poly * tot_non / tot
]
for obs, ex in zip(site_counts, exp):
G += obs * log(obs / ex)
G *= 2
# return 1-chi2.cdf(G, 1) # only 1 dof for 2x2 table
return chisqprob(G, 1)
def _G_test(site_counts):
"""G test for 2x2 contingency table (PRIVATE).
Argument:
- site_counts - [syn_fix, nonsyn_fix, syn_poly, nonsyn_poly]
>>> round(_G_test([17, 7, 42, 2]), 7)
0.004924
"""
# TODO:
# Apply continuity correction for Chi-square test.
from math import log
# from scipy.stats import chi2
G = 0
tot = sum(site_counts)
tot_syn = site_counts[0] + site_counts[2]
tot_non = site_counts[1] + site_counts[3]
tot_fix = sum(site_counts[:2])
tot_poly = sum(site_counts[2:])
exp = [tot_fix * tot_syn / tot, tot_fix * tot_non / tot,
tot_poly * tot_syn / tot, tot_poly * tot_non / tot]
for obs, ex in zip(site_counts, exp):
G += obs * log(obs / ex)
G *= 2
# return 1-chi2.cdf(G, 1) # only 1 dof for 2x2 table
return chisqprob(G, 1)
