Refactor fmt_p
Combine html, only_value, tabular flags into a single Flag
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@ -13,6 +13,26 @@ Data wrangling
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.. autofunction:: yli.utils.fmt_p
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.. autoclass:: yli.utils.PValueStyle
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.. attribute:: VALUE_ONLY
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Display only the *p* value (e.g. ``0.08``, ``<0.001*``)
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This is an alias for specifying no flags.
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.. attribute:: RELATION
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Force displaying a relational operator before the *p* value (e.g. ``= 0.08``, ``< 0.001*``)
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.. attribute:: TABULAR
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Pad with spaces to ensure decimal points align (incompatible with :attr:`RELATION`)
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.. attribute:: HTML
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Format as HTML (i.e. escape ``<``)
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Formula manipulation
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--------------------
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@ -16,7 +16,7 @@
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import yli
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from yli.config import config
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from yli.utils import fmt_p
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from yli.utils import PValueStyle, fmt_p
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def test_fmt_pvalues_ord():
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"""Test formatting of p values requiring no special handling"""
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@ -27,11 +27,11 @@ def test_fmt_pvalues_ord():
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config.pvalue_leading_zero = True
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config.alpha = 0.05
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assert fmt_p(0.0096, html=False) == '= 0.01*'
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assert fmt_p(0.01, html=False) == '= 0.01*'
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assert fmt_p(0.04, html=False) == '= 0.04*'
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assert fmt_p(0.11, html=False) == '= 0.11'
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assert fmt_p(0.55, html=False) == '= 0.55'
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assert fmt_p(0.0096, PValueStyle.RELATION) == '= 0.01*'
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assert fmt_p(0.01, PValueStyle.RELATION) == '= 0.01*'
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assert fmt_p(0.04, PValueStyle.RELATION) == '= 0.04*'
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assert fmt_p(0.11, PValueStyle.RELATION) == '= 0.11'
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assert fmt_p(0.55, PValueStyle.RELATION) == '= 0.55'
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def test_fmt_pvalues_ord_noleadingzero():
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"""Test formatting of p values requiring no special handling, no leading zero"""
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@ -42,11 +42,11 @@ def test_fmt_pvalues_ord_noleadingzero():
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config.pvalue_leading_zero = False
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config.alpha = 0.05
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assert fmt_p(0.0096, html=False) == '= .01*'
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assert fmt_p(0.01, html=False) == '= .01*'
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assert fmt_p(0.04, html=False) == '= .04*'
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assert fmt_p(0.11, html=False) == '= .11'
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assert fmt_p(0.55, html=False) == '= .55'
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assert fmt_p(0.0096, PValueStyle.RELATION) == '= .01*'
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assert fmt_p(0.01, PValueStyle.RELATION) == '= .01*'
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assert fmt_p(0.04, PValueStyle.RELATION) == '= .04*'
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assert fmt_p(0.11, PValueStyle.RELATION) == '= .11'
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assert fmt_p(0.55, PValueStyle.RELATION) == '= .55'
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def test_fmt_pvalues_small():
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"""Test formatting of small p values requiring extra decimal points to represent"""
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@ -57,7 +57,7 @@ def test_fmt_pvalues_small():
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config.pvalue_leading_zero = True
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config.alpha = 0.05
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assert fmt_p(0.009, html=False) == '= 0.009*'
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assert fmt_p(0.009, PValueStyle.RELATION) == '= 0.009*'
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def test_fmt_pvalues_ambiguous():
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"""Test formatting of p values requiring extra decimal points to avoid ambiguity"""
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@ -68,12 +68,12 @@ def test_fmt_pvalues_ambiguous():
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config.pvalue_leading_zero = True
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config.alpha = 0.05
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assert fmt_p(0.048, html=False) == '= 0.048*'
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assert fmt_p(0.052, html=False) == '= 0.052'
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assert fmt_p(0.048, PValueStyle.RELATION) == '= 0.048*'
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assert fmt_p(0.052, PValueStyle.RELATION) == '= 0.052'
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# Special rounding rules
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assert fmt_p(0.04999, html=False) == '= 0.049*'
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assert fmt_p(0.05001, html=False) == '= 0.051'
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assert fmt_p(0.04999, PValueStyle.RELATION) == '= 0.049*'
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assert fmt_p(0.05001, PValueStyle.RELATION) == '= 0.051'
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def test_fmt_pvalues_extreme():
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"""Test formatting of p values too small or large to be represented"""
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@ -84,5 +84,5 @@ def test_fmt_pvalues_extreme():
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config.pvalue_leading_zero = True
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config.alpha = 0.05
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assert fmt_p(0.0009, html=False) == '< 0.001*'
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assert fmt_p(0.999, html=False) == '> 0.99'
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assert fmt_p(0.0009, PValueStyle.RELATION) == '< 0.001*'
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assert fmt_p(0.999, PValueStyle.RELATION) == '> 0.99'
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@ -29,7 +29,7 @@ import warnings
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from .bayes_factors import BayesFactor, bayesfactor_afbf
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from .config import config
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from .sig_tests import FTestResult
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from .utils import Estimate, check_nan, cols_for_formula, convert_pandas_nullable, fmt_p, formula_factor_ref_category, parse_patsy_term
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from .utils import Estimate, PValueStyle, check_nan, cols_for_formula, convert_pandas_nullable, fmt_p, formula_factor_ref_category, parse_patsy_term
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def vif(df, formula=None, *, nan_policy='warn'):
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"""
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@ -112,7 +112,7 @@ class LikelihoodRatioTestResult:
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return super().__repr__()
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def _repr_html_(self):
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return 'LR({}) = {:.2f}; <i>p</i> {}'.format(self.dof, self.statistic, fmt_p(self.pvalue, html=True))
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return 'LR({}) = {:.2f}; <i>p</i> {}'.format(self.dof, self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION | PValueStyle.HTML))
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def summary(self):
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"""
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@ -121,7 +121,7 @@ class LikelihoodRatioTestResult:
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:rtype: str
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"""
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return 'LR({}) = {:.2f}; p {}'.format(self.dof, self.statistic, fmt_p(self.pvalue, html=False))
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return 'LR({}) = {:.2f}; p {}'.format(self.dof, self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION))
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class RegressionResult:
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"""
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@ -272,10 +272,10 @@ class RegressionResult:
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if html:
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right_col.append(('<i>F</i>:', format(f_result.statistic, '.2f')))
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right_col.append(('<i>p</i> (<i>F</i>):', fmt_p(f_result.pvalue, html=True, only_value=True)))
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right_col.append(('<i>p</i> (<i>F</i>):', fmt_p(f_result.pvalue, PValueStyle.VALUE_ONLY | PValueStyle.HTML)))
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else:
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right_col.append(('F:', format(f_result.statistic, '.2f')))
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right_col.append(('p (F):', fmt_p(f_result.pvalue, html=False, only_value=True)))
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right_col.append(('p (F):', fmt_p(f_result.pvalue, PValueStyle.VALUE_ONLY)))
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else:
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# Otherwise report likelihood ratio test as overall test
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lrtest_result = self.lrtest_null()
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@ -283,9 +283,9 @@ class RegressionResult:
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right_col.append(('LL-Model:', format(self.llf, '.2f')))
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right_col.append(('LL-Null:', format(self.llnull, '.2f')))
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if html:
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right_col.append(('<i>p</i> (LR):', fmt_p(lrtest_result.pvalue, html=True, only_value=True)))
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right_col.append(('<i>p</i> (LR):', fmt_p(lrtest_result.pvalue, PValueStyle.VALUE_ONLY | PValueStyle.HTML)))
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else:
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right_col.append(('p (LR):', fmt_p(lrtest_result.pvalue, html=False, only_value=True)))
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right_col.append(('p (LR):', fmt_p(lrtest_result.pvalue, PValueStyle.VALUE_ONLY)))
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return left_col, right_col
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@ -320,7 +320,7 @@ class RegressionResult:
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if self.exp:
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beta = np.exp(beta)
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out += '<tr><th>{}</th><td>{:.2f}</td><td style="padding-right:0">({:.2f}</td><td>–</td><td style="padding-left:0">{:.2f})</td><td style="text-align:left">{}</td></tr>'.format(term_name, beta.point, beta.ci_lower, beta.ci_upper, fmt_p(term.pvalue, html=True, tabular=True))
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out += '<tr><th>{}</th><td>{:.2f}</td><td style="padding-right:0">({:.2f}</td><td>–</td><td style="padding-left:0">{:.2f})</td><td style="text-align:left">{}</td></tr>'.format(term_name, beta.point, beta.ci_lower, beta.ci_upper, fmt_p(term.pvalue, PValueStyle.TABULAR | PValueStyle.HTML))
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elif isinstance(term, CategoricalTerm):
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# Categorical term
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out += '<tr><th>{}</th><td></td><td style="padding-right:0"></td><td></td><td style="padding-left:0"></td><td></td></tr>'.format(term_name)
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@ -335,7 +335,7 @@ class RegressionResult:
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if self.exp:
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beta = np.exp(beta)
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out += '<tr><td style="text-align:right;font-style:italic">{}</td><td>{:.2f}</td><td style="padding-right:0">({:.2f}</td><td>–</td><td style="padding-left:0">{:.2f})</td><td style="text-align:left">{}</td></tr>'.format(sub_term_name, beta.point, beta.ci_lower, beta.ci_upper, fmt_p(sub_term.pvalue, html=True, tabular=True))
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out += '<tr><td style="text-align:right;font-style:italic">{}</td><td>{:.2f}</td><td style="padding-right:0">({:.2f}</td><td>–</td><td style="padding-left:0">{:.2f})</td><td style="text-align:left">{}</td></tr>'.format(sub_term_name, beta.point, beta.ci_lower, beta.ci_upper, fmt_p(sub_term.pvalue, PValueStyle.TABULAR | PValueStyle.HTML))
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else:
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raise Exception('Attempt to render unknown term type')
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@ -381,7 +381,7 @@ class RegressionResult:
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beta = np.exp(beta)
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# Add some extra padding
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table_data.append([term_name + ' ', format(beta.point, '.2f'), '({:.2f}'.format(beta.ci_lower), '-', '{:.2f})'.format(beta.ci_upper), ' ' + fmt_p(term.pvalue, html=False, tabular=True)])
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table_data.append([term_name + ' ', format(beta.point, '.2f'), '({:.2f}'.format(beta.ci_lower), '-', '{:.2f})'.format(beta.ci_upper), ' ' + fmt_p(term.pvalue, PValueStyle.TABULAR)])
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elif isinstance(term, CategoricalTerm):
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# Categorical term
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table_data.append([term_name + ' ', '', '', '', '', ''])
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@ -396,7 +396,7 @@ class RegressionResult:
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if self.exp:
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beta = np.exp(beta)
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table_data.append([sub_term_name + ' ', format(beta.point, '.2f'), '({:.2f}'.format(beta.ci_lower), '-', '{:.2f})'.format(beta.ci_upper), ' ' + fmt_p(sub_term.pvalue, html=False, tabular=True)])
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table_data.append([sub_term_name + ' ', format(beta.point, '.2f'), '({:.2f}'.format(beta.ci_lower), '-', '{:.2f})'.format(beta.ci_upper), ' ' + fmt_p(sub_term.pvalue, PValueStyle.TABULAR)])
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else:
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raise Exception('Attempt to render unknown term type')
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@ -23,7 +23,7 @@ import functools
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import warnings
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from .config import config
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from .utils import Estimate, as_2groups, check_nan, convert_pandas_nullable, fmt_p
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from .utils import Estimate, PValueStyle, as_2groups, check_nan, convert_pandas_nullable, fmt_p
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# ----------------
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# Student's t test
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@ -65,7 +65,7 @@ class TTestResult:
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return super().__repr__()
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def _repr_html_(self):
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return '<i>t</i>({:.0f}) = {:.2f}; <i>p</i> {}<br><i>μ</i><sub>{}</sub> (SD) = {:.2f} ({:.2f}), <i>μ</i><sub>{}</sub> (SD) = {:.2f} ({:.2f})<br>Δ<i>μ</i> ({:g}% CI) = {}, {}'.format(self.dof, self.statistic, fmt_p(self.pvalue, html=True), self.group1, self.mu1, self.sd1, self.group2, self.mu2, self.sd2, (1-config.alpha)*100, self.delta.summary(), self.delta_direction)
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return '<i>t</i>({:.0f}) = {:.2f}; <i>p</i> {}<br><i>μ</i><sub>{}</sub> (SD) = {:.2f} ({:.2f}), <i>μ</i><sub>{}</sub> (SD) = {:.2f} ({:.2f})<br>Δ<i>μ</i> ({:g}% CI) = {}, {}'.format(self.dof, self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION | PValueStyle.HTML), self.group1, self.mu1, self.sd1, self.group2, self.mu2, self.sd2, (1-config.alpha)*100, self.delta.summary(), self.delta_direction)
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def summary(self):
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"""
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@ -74,7 +74,7 @@ class TTestResult:
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:rtype: str
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"""
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return 't({:.0f}) = {:.2f}; p {}\nμ({}) (SD) = {:.2f} ({:.2f}), μ({}) (SD) = {:.2f} ({:.2f})\nΔμ ({:g}% CI) = {}, {}'.format(self.dof, self.statistic, fmt_p(self.pvalue, html=False), self.group1, self.mu1, self.sd1, self.group2, self.mu2, self.sd2, (1-config.alpha)*100, self.delta.summary(), self.delta_direction)
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return 't({:.0f}) = {:.2f}; p {}\nμ({}) (SD) = {:.2f} ({:.2f}), μ({}) (SD) = {:.2f} ({:.2f})\nΔμ ({:g}% CI) = {}, {}'.format(self.dof, self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION), self.group1, self.mu1, self.sd1, self.group2, self.mu2, self.sd2, (1-config.alpha)*100, self.delta.summary(), self.delta_direction)
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def ttest_ind(df, dep, ind, *, nan_policy='warn'):
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"""
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@ -166,7 +166,7 @@ class FTestResult:
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return super().__repr__()
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def _repr_html_(self):
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return '<i>F</i>({:.0f}, {:.0f}) = {:.2f}; <i>p</i> {}'.format(self.dof1, self.dof2, self.statistic, fmt_p(self.pvalue, html=True))
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return '<i>F</i>({:.0f}, {:.0f}) = {:.2f}; <i>p</i> {}'.format(self.dof1, self.dof2, self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION | PValueStyle.HTML))
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def summary(self):
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"""
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@ -175,7 +175,7 @@ class FTestResult:
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:rtype: str
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"""
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return 'F({:.0f}, {:.0f}) = {:.2f}; p {}'.format(self.dof1, self.dof2, self.statistic, fmt_p(self.pvalue, html=False))
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return 'F({:.0f}, {:.0f}) = {:.2f}; p {}'.format(self.dof1, self.dof2, self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION))
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def anova_oneway(df, dep, ind, *, nan_policy='omit'):
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"""
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@ -252,7 +252,7 @@ class MannWhitneyResult:
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return super().__repr__()
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def _repr_html_(self):
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line1 = '<i>U</i> = {:.1f}; <i>p</i> {}<br><i>r</i> = {:.2f}, {}'.format(self.statistic, fmt_p(self.pvalue, html=True), self.rank_biserial, self.direction)
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line1 = '<i>U</i> = {:.1f}; <i>p</i> {}<br><i>r</i> = {:.2f}, {}'.format(self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION | PValueStyle.HTML), self.rank_biserial, self.direction)
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if self.brunnermunzel:
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return line1 + '<br>' + self.brunnermunzel._repr_html_()
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else:
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@ -265,7 +265,7 @@ class MannWhitneyResult:
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:rtype: str
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"""
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line1 = 'U = {:.1f}; p {}\nr = {:.2f}, {}'.format(self.statistic, fmt_p(self.pvalue, html=False), self.rank_biserial, self.direction)
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line1 = 'U = {:.1f}; p {}\nr = {:.2f}, {}'.format(self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION), self.rank_biserial, self.direction)
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if self.brunnermunzel:
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return line1 + '\n' + self.brunnermunzel.summary()
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else:
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@ -292,7 +292,7 @@ class BrunnerMunzelResult:
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return super().__repr__()
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def _repr_html_(self):
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return '<i>W</i> = {:.1f}; <i>p</i> {}'.format(self.statistic, fmt_p(self.pvalue, html=True))
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return '<i>W</i> = {:.1f}; <i>p</i> {}'.format(self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION | PValueStyle.HTML))
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def summary(self):
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"""
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@ -301,7 +301,7 @@ class BrunnerMunzelResult:
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:rtype: str
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"""
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return 'W = {:.1f}; p {}'.format(self.statistic, fmt_p(self.pvalue, html=False))
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return 'W = {:.1f}; p {}'.format(self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION))
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def mannwhitney(df, dep, ind, *, nan_policy='warn', brunnermunzel=True, use_continuity=False, alternative='two-sided', method='auto'):
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"""
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@ -415,10 +415,10 @@ class PearsonChiSquaredResult:
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def _repr_html_(self):
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if self.oddsratio is not None:
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return '{0}<br><i>χ</i><sup>2</sup>({1}) = {2:.2f}; <i>p</i> {3}<br>OR ({4:g}% CI) = {5}<br>RR ({4:g}% CI) = {6}'.format(
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self.ct._repr_html_(), self.dof, self.statistic, fmt_p(self.pvalue, html=True), (1-config.alpha)*100, self.oddsratio.summary(), self.riskratio.summary())
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self.ct._repr_html_(), self.dof, self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION | PValueStyle.HTML), (1-config.alpha)*100, self.oddsratio.summary(), self.riskratio.summary())
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else:
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return '{}<br><i>χ</i><sup>2</sup>({}) = {:.2f}; <i>p</i> {}'.format(
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self.ct._repr_html_(), self.dof, self.statistic, fmt_p(self.pvalue, html=True))
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self.ct._repr_html_(), self.dof, self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION | PValueStyle.HTML))
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def summary(self):
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"""
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@ -429,10 +429,10 @@ class PearsonChiSquaredResult:
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if self.oddsratio is not None:
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return '{0}\n\nχ²({1}) = {2:.2f}; p {3}\nOR ({4:g}% CI) = {5}\nRR ({4:g}% CI) = {6}'.format(
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self.ct, self.dof, self.statistic, fmt_p(self.pvalue, html=False), (1-config.alpha)*100, self.oddsratio.summary(), self.riskratio.summary())
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self.ct, self.dof, self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION), (1-config.alpha)*100, self.oddsratio.summary(), self.riskratio.summary())
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else:
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return '{}\n\nχ²({}) = {:.2f}; p {}'.format(
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self.ct, self.dof, self.statistic, fmt_p(self.pvalue, html=False))
|
||||
self.ct, self.dof, self.statistic, fmt_p(self.pvalue, PValueStyle.RELATION))
|
||||
|
||||
def chi2(df, dep, ind, *, nan_policy='warn'):
|
||||
"""
|
||||
@ -538,7 +538,7 @@ class PearsonRResult:
|
||||
return super().__repr__()
|
||||
|
||||
def _repr_html_(self):
|
||||
return '<i>r</i> ({:g}% CI) = {}; <i>p</i> {}'.format((1-config.alpha)*100, self.statistic.summary(), fmt_p(self.pvalue, html=True))
|
||||
return '<i>r</i> ({:g}% CI) = {}; <i>p</i> {}'.format((1-config.alpha)*100, self.statistic.summary(), fmt_p(self.pvalue, PValueStyle.RELATION | PValueStyle.HTML))
|
||||
|
||||
def summary(self):
|
||||
"""
|
||||
@ -547,7 +547,7 @@ class PearsonRResult:
|
||||
:rtype: str
|
||||
"""
|
||||
|
||||
return 'r ({:g}% CI) = {}; p {}'.format((1-config.alpha)*100, self.statistic.summary(), fmt_p(self.pvalue, html=False))
|
||||
return 'r ({:g}% CI) = {}; p {}'.format((1-config.alpha)*100, self.statistic.summary(), fmt_p(self.pvalue, PValueStyle.RELATION))
|
||||
|
||||
def pearsonr(df, dep, ind, *, nan_policy='warn'):
|
||||
"""
|
||||
|
||||
50
yli/utils.py
50
yli/utils.py
@ -18,6 +18,7 @@ import numpy as np
|
||||
import pandas as pd
|
||||
import patsy
|
||||
|
||||
import enum
|
||||
import warnings
|
||||
|
||||
from .config import config
|
||||
@ -145,25 +146,28 @@ def do_fmt_p(p):
|
||||
# OK to round to pvalue_min_dps
|
||||
return '', '{0:.{dps}f}'.format(p, dps=config.pvalue_min_dps)
|
||||
|
||||
def fmt_p(p, *, html, only_value=False, tabular=False):
|
||||
class PValueStyle(enum.Flag):
|
||||
"""An *enum.Flag* representing how to render a *p* value"""
|
||||
|
||||
VALUE_ONLY = 0
|
||||
|
||||
RELATION = enum.auto()
|
||||
TABULAR = enum.auto()
|
||||
HTML = enum.auto()
|
||||
|
||||
def fmt_p(p, style):
|
||||
"""
|
||||
Format *p* value for display
|
||||
|
||||
:param p: *p* value to display
|
||||
:type p: float
|
||||
:param html: Whether to output as HTML (*True*) or plaintext (*False*)
|
||||
:type html: bool
|
||||
:param only_value: Whether to display only the value (*True*, e.g. ``0.04``, ``<0.001``) or equality symbol and value (*False*, e.g. ``= 0.04``, ``< 0.001``)
|
||||
:type only_value: bool
|
||||
:param tabular: Whether to pad with spaces so that decimal points align
|
||||
:type tabular: bool
|
||||
:param style: Style to format the *p* value
|
||||
:type style: :class:`PValueStyle`
|
||||
|
||||
:return: Formatted *p* value
|
||||
:rtype: str
|
||||
"""
|
||||
|
||||
# FIXME: Make only_value and tabular enums
|
||||
|
||||
sign, fmt = do_fmt_p(p)
|
||||
|
||||
# Strip leading zero if required
|
||||
@ -176,28 +180,32 @@ def fmt_p(p, *, html, only_value=False, tabular=False):
|
||||
else:
|
||||
asterisk = ''
|
||||
|
||||
if html:
|
||||
if PValueStyle.HTML in style:
|
||||
# Escape angle quotes
|
||||
sign = sign.replace('<', '<')
|
||||
sign = sign.replace('>', '>')
|
||||
|
||||
if only_value:
|
||||
return '{}{}{}'.format(sign, fmt, asterisk)
|
||||
elif tabular:
|
||||
if PValueStyle.RELATION in style:
|
||||
# Add relational operator
|
||||
if not sign:
|
||||
sign = '='
|
||||
return '{} {}{}'.format(sign, fmt, asterisk)
|
||||
elif PValueStyle.TABULAR in style:
|
||||
# Always left-aligned, so reserve space for sign if required to align decimal points
|
||||
if not sign:
|
||||
sign = '<span style="visibility:hidden">=</span>'
|
||||
|
||||
return '{}{}{}'.format(sign, fmt, asterisk)
|
||||
else:
|
||||
# Non-tabular so force a sign
|
||||
# Only value
|
||||
return '{}{}{}'.format(sign, fmt, asterisk)
|
||||
else:
|
||||
if PValueStyle.RELATION in style:
|
||||
# Add relational operator
|
||||
if not sign:
|
||||
sign = '='
|
||||
return '{} {}{}'.format(sign, fmt, asterisk)
|
||||
else:
|
||||
if only_value:
|
||||
return '{}{}{}'.format(sign, fmt, asterisk)
|
||||
elif tabular:
|
||||
elif PValueStyle.TABULAR in style:
|
||||
# Right-aligned, so add spaces to simulate left alignment
|
||||
if not sign:
|
||||
sign = ' '
|
||||
@ -214,10 +222,8 @@ def fmt_p(p, *, html, only_value=False, tabular=False):
|
||||
|
||||
return '{}{}{}{}'.format(sign, fmt, asterisk, rpadding)
|
||||
else:
|
||||
# Non-tabular so force a sign
|
||||
if not sign:
|
||||
sign = '='
|
||||
return '{} {}{}'.format(sign, fmt, asterisk)
|
||||
# Only value
|
||||
return '{}{}{}'.format(sign, fmt, asterisk)
|
||||
|
||||
# ------------------------------
|
||||
# General result-related classes
|
||||
|
||||
Loading…
Reference in New Issue
Block a user