def summary(self, alpha=0.05, float_format="%.3f", method="normal"):
"""
A summary of all the main results.
Parameters
----------
alpha : float
`1 - alpha` is the nominal coverage probability of the
confidence intervals.
float_format : str
Used for formatting numeric values in the summary.
method : str
The method for producing the confidence interval. Currently
must be 'normal' which uses the normal approximation.
"""
def fmt(x):
if isinstance(x, str):
return x
return float_format % x
co_lcb, co_ucb = self.oddsratio_pooled_confint(alpha=alpha,
method=method)
clo_lcb, clo_ucb = self.logodds_pooled_confint(alpha=alpha,
method=method)
headers = ["Estimate", "LCB", "UCB"]
stubs = ["Pooled odds", "Pooled log odds", "Pooled risk ratio", ""]
data = [[fmt(x) for x in [self.oddsratio_pooled, co_lcb, co_ucb]],
[fmt(x) for x in [self.logodds_pooled, clo_lcb, clo_ucb]],
[fmt(x) for x in [self.riskratio_pooled, "", ""]],
['', '', '']]
tab1 = iolib.SimpleTable(data,
headers,
stubs,
data_aligns="r",
table_dec_above='')
headers = ["Statistic", "P-value", ""]
stubs = ["Test of OR=1", "Test constant OR"]
rslt1 = self.test_null_odds()
rslt2 = self.test_equal_odds()
data = [[fmt(x) for x in [rslt1.statistic, rslt1.pvalue, ""]],
[fmt(x) for x in [rslt2.statistic, rslt2.pvalue, ""]]]
tab2 = iolib.SimpleTable(data, headers, stubs, data_aligns="r")
tab1.extend(tab2)
headers = ["", "", ""]
stubs = ["Number of tables", "Min n", "Max n", "Avg n", "Total n"]
ss = self.table.sum(0).sum(0)
data = [["%d" % self.table.shape[2], '', ''], ["%d" % min(ss), '', ''],
["%d" % max(ss), '', ''], ["%.0f" % np.mean(ss), '', ''],
["%d" % sum(ss), '', '', '']]
tab3 = iolib.SimpleTable(data, headers, stubs, data_aligns="r")
tab1.extend(tab3)
return tab1
def summary(self, alpha=0.05, float_format="%.3f"):
"""
Produce a summary of the analysis.
Parameters
----------
alpha : float
`1 - alpha` is the nominal coverage probability of the interval.
float_format : str
Used to format numeric values in the table.
method : str
The method for producing the confidence interval. Currently
must be 'normal' which uses the normal approximation.
"""
fmt = float_format
headers = ["Statistic", "P-value", "DF"]
stubs = ["Symmetry", "Homogeneity"]
sy = self.symmetry()
hm = self.homogeneity()
data = [[fmt % sy.statistic, fmt % sy.pvalue,
'%d' % sy.df],
[fmt % hm.statistic, fmt % hm.pvalue,
'%d' % hm.df]]
tab = iolib.SimpleTable(data,
headers,
stubs,
data_aligns="r",
table_dec_above='')
return tab
def summary(self, alpha=0.05, float_format="%.3f", method="normal"):
"""
Summarizes results for a 2x2 table analysis.
Parameters
----------
alpha : float
`1 - alpha` is the nominal coverage probability of the confidence
intervals.
float_format : str
Used to format the numeric values in the table.
method : str
The method for producing the confidence interval. Currently
must be 'normal' which uses the normal approximation.
"""
def fmt(x):
if isinstance(x, str):
return x
return float_format % x
headers = ["Estimate", "SE", "LCB", "UCB", "p-value"]
stubs = [
"Odds ratio", "Log odds ratio", "Risk ratio", "Log risk ratio"
]
lcb1, ucb1 = self.oddsratio_confint(alpha, method)
lcb2, ucb2 = self.log_oddsratio_confint(alpha, method)
lcb3, ucb3 = self.riskratio_confint(alpha, method)
lcb4, ucb4 = self.log_riskratio_confint(alpha, method)
data = [[
fmt(x)
for x in [self.oddsratio, "", lcb1, ucb1,
self.oddsratio_pvalue()]
],
[
fmt(x) for x in [
self.log_oddsratio, self.log_oddsratio_se, lcb2, ucb2,
self.oddsratio_pvalue()
]
],
[
fmt(x) for x in
[self.riskratio, "", lcb3, ucb3,
self.riskratio_pvalue()]
],
[
fmt(x) for x in [
self.log_riskratio, self.log_riskratio_se, lcb4, ucb4,
self.riskratio_pvalue()
]
]]
tab = iolib.SimpleTable(data,
headers,
stubs,
data_aligns="r",
table_dec_above='')
return tab
