def test_alternative(case):
# regression test numbers, but those are close to each other
alt, meth = case
count1, n1, count2, n2 = 6, 51., 1, 54.
_, pv = smr.test_poisson_2indep(count1, n1, count2, n2, method=meth,
ratio_null=1.2, alternative=alt)
assert_allclose(pv, cases_alt[case], rtol=1e-13)
def test_twosample_poisson_r():
# testing against R package `exactci
from .results.results_rates import res_pexact_cond, res_pexact_cond_midp
# example 1 from Gu
count1, n1, count2, n2 = 60, 51477.5, 30, 54308.7
res2 = res_pexact_cond
res1 = smr.test_poisson_2indep(count1, n1, count2, n2, method='exact-cond')
assert_allclose(res1.pvalue, res2.p_value, rtol=1e-13)
assert_allclose(res1.ratio, res2.estimate, rtol=1e-13)
assert_equal(res1.ratio_null, res2.null_value)
res2 = res_pexact_cond_midp
res1 = smr.test_poisson_2indep(count1, n1, count2, n2, method='cond-midp')
assert_allclose(res1.pvalue, res2.p_value, rtol=0, atol=5e-6)
assert_allclose(res1.ratio, res2.estimate, rtol=1e-13)
assert_equal(res1.ratio_null, res2.null_value)
# one-sided
# > pe = poisson.exact(c(60, 30), c(51477.5, 54308.7), r=1.2,
# alternative="less", tsmethod="minlike", midp=TRUE)
# > pe$p.value
pv2 = 0.9949053964701466
rest = smr.test_poisson_2indep(count1, n1, count2, n2, method='cond-midp',
ratio_null=1.2, alternative='smaller')
assert_allclose(rest.pvalue, pv2, rtol=1e-12)
# > pe = poisson.exact(c(60, 30), c(51477.5, 54308.7), r=1.2,
# alternative="greater", tsmethod="minlike", midp=TRUE)
# > pe$p.value
pv2 = 0.005094603529853279
rest = smr.test_poisson_2indep(count1, n1, count2, n2, method='cond-midp',
ratio_null=1.2, alternative='larger')
assert_allclose(rest.pvalue, pv2, rtol=1e-12)
# > pe = poisson.exact(c(60, 30), c(51477.5, 54308.7), r=1.2,
# alternative="greater", tsmethod="minlike", midp=FALSE)
# > pe$p.value
pv2 = 0.006651774552714537
rest = smr.test_poisson_2indep(count1, n1, count2, n2, method='exact-cond',
ratio_null=1.2, alternative='larger')
assert_allclose(rest.pvalue, pv2, rtol=1e-12)
# > pe = poisson.exact(c(60, 30), c(51477.5, 54308.7), r=1.2,
# alternative="less", tsmethod="minlike", midp=FALSE)
# > pe$p.value
pv2 = 0.9964625674930079
rest = smr.test_poisson_2indep(count1, n1, count2, n2, method='exact-cond',
ratio_null=1.2, alternative='smaller')
assert_allclose(rest.pvalue, pv2, rtol=1e-12)
def test_twosample_poisson():
# testing against two examples in Gu et al
# example 1
count1, n1, count2, n2 = 60, 51477.5, 30, 54308.7
s1, pv1 = smr.test_poisson_2indep(count1, n1, count2, n2, method='wald')
pv1r = 0.000356
assert_allclose(pv1, pv1r * 2, rtol=0, atol=5e-6)
assert_allclose(s1, 3.384913, atol=0, rtol=5e-6) # regression test
s2, pv2 = smr.test_poisson_2indep(count1, n1, count2, n2, method='score')
pv2r = 0.000316
assert_allclose(pv2, pv2r * 2, rtol=0, atol=5e-6)
assert_allclose(s2, 3.417402, atol=0, rtol=5e-6) # regression test
s2, pv2 = smr.test_poisson_2indep(count1, n1, count2, n2, method='sqrt')
pv2r = 0.000285
assert_allclose(pv2, pv2r * 2, rtol=0, atol=5e-6)
assert_allclose(s2, 3.445485, atol=0, rtol=5e-6) # regression test
# two-sided
# example2
# I don't know why it's only 2.5 decimal agreement, rounding?
count1, n1, count2, n2 = 41, 28010, 15, 19017
s1, pv1 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='wald',
ratio_null=1.5)
pv1r = 0.2309
assert_allclose(pv1, pv1r * 2, rtol=0, atol=5e-3)
assert_allclose(s1, 0.735447, atol=0, rtol=5e-6) # regression test
s2, pv2 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='score',
ratio_null=1.5)
pv2r = 0.2398
assert_allclose(pv2, pv2r * 2, rtol=0, atol=5e-3)
assert_allclose(s2, 0.706631, atol=0, rtol=5e-6) # regression test
s2, pv2 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='sqrt',
ratio_null=1.5)
pv2r = 0.2499
assert_allclose(pv2, pv2r * 2, rtol=0, atol=5e-3)
assert_allclose(s2, 0.674401, atol=0, rtol=5e-6) # regression test
# one-sided
# example 1 onesided
count1, n1, count2, n2 = 60, 51477.5, 30, 54308.7
s1, pv1 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='wald',
alternative='larger')
pv1r = 0.000356
assert_allclose(pv1, pv1r, rtol=0, atol=5e-6)
s2, pv2 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='score',
alternative='larger')
pv2r = 0.000316
assert_allclose(pv2, pv2r, rtol=0, atol=5e-6)
s2, pv2 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='sqrt',
alternative='larger')
pv2r = 0.000285
assert_allclose(pv2, pv2r, rtol=0, atol=5e-6)
# 'exact-cond', 'cond-midp'
s2, pv2 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='exact-cond',
ratio_null=1,
alternative='larger')
pv2r = 0.000428 # typo in Gu et al, switched pvalues between C and M
assert_allclose(pv2, pv2r, rtol=0, atol=5e-4)
s2, pv2 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='cond-midp',
ratio_null=1,
alternative='larger')
pv2r = 0.000310
assert_allclose(pv2, pv2r, rtol=0, atol=5e-4)
_, pve1 = etest_poisson_2indep(count1,
n1,
count2,
n2,
method='score',
ratio_null=1,
alternative='larger')
pve1r = 0.000298
assert_allclose(pve1, pve1r, rtol=0, atol=5e-4)
_, pve1 = etest_poisson_2indep(count1,
n1,
count2,
n2,
method='wald',
ratio_null=1,
alternative='larger')
pve1r = 0.000298
assert_allclose(pve1, pve1r, rtol=0, atol=5e-4)
# example2 onesided
# I don't know why it's only 2.5 decimal agreement, rounding?
count1, n1, count2, n2 = 41, 28010, 15, 19017
s1, pv1 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='wald',
ratio_null=1.5,
alternative='larger')
pv1r = 0.2309
assert_allclose(pv1, pv1r, rtol=0, atol=5e-4)
s2, pv2 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='score',
ratio_null=1.5,
alternative='larger')
pv2r = 0.2398
assert_allclose(pv2, pv2r, rtol=0, atol=5e-4)
s2, pv2 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='sqrt',
ratio_null=1.5,
alternative='larger')
pv2r = 0.2499
assert_allclose(pv2, pv2r, rtol=0, atol=5e-4)
# 'exact-cond', 'cond-midp'
s2, pv2 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='exact-cond',
ratio_null=1.5,
alternative='larger')
pv2r = 0.2913
assert_allclose(pv2, pv2r, rtol=0, atol=5e-4)
s2, pv2 = smr.test_poisson_2indep(count1,
n1,
count2,
n2,
method='cond-midp',
ratio_null=1.5,
alternative='larger')
pv2r = 0.2450
assert_allclose(pv2, pv2r, rtol=0, atol=5e-4)
_, pve2 = etest_poisson_2indep(count1,
n1,
count2,
n2,
method='score',
ratio_null=1.5,
alternative='larger')
pve2r = 0.2453
assert_allclose(pve2, pve2r, rtol=0, atol=5e-4)
_, pve2 = etest_poisson_2indep(count1,
n1,
count2,
n2,
method='wald',
ratio_null=1.5,
alternative='larger')
pve2r = 0.2453
assert_allclose(pve2, pve2r, rtol=0, atol=5e-4)