Allow customising p value formatting

tests/test_fmt_pvalues.py

@@ -0,0 +1,88 @@
+#   scipy-yli: Helpful SciPy utilities and recipes
+#   Copyright © 2022  Lee Yingtong Li (RunasSudo)
+#
+#   This program is free software: you can redistribute it and/or modify
+#   it under the terms of the GNU Affero General Public License as published by
+#   the Free Software Foundation, either version 3 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU Affero General Public License for more details.
+#
+#   You should have received a copy of the GNU Affero General Public License
+#   along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+import yli
+from yli.config import config
+from yli.utils import fmt_p
+
+def test_fmt_pvalues_ord():
+	"""Test formatting of p values requiring no special handling"""
+	
+	# Default config
+	config.pvalue_min_dps = 2
+	config.pvalue_max_dps = 3
+	config.pvalue_leading_zero = True
+	config.alpha = 0.05
+	
+	assert fmt_p(0.0096, html=False) == '= 0.01*'
+	assert fmt_p(0.01, html=False) == '= 0.01*'
+	assert fmt_p(0.04, html=False) == '= 0.04*'
+	assert fmt_p(0.11, html=False) == '= 0.11'
+	assert fmt_p(0.55, html=False) == '= 0.55'
+
+def test_fmt_pvalues_ord_noleadingzero():
+	"""Test formatting of p values requiring no special handling, no leading zero"""
+	
+	# Default config
+	config.pvalue_min_dps = 2
+	config.pvalue_max_dps = 3
+	config.pvalue_leading_zero = False
+	config.alpha = 0.05
+	
+	assert fmt_p(0.0096, html=False) == '= .01*'
+	assert fmt_p(0.01, html=False) == '= .01*'
+	assert fmt_p(0.04, html=False) == '= .04*'
+	assert fmt_p(0.11, html=False) == '= .11'
+	assert fmt_p(0.55, html=False) == '= .55'
+
+def test_fmt_pvalues_small():
+	"""Test formatting of small p values requiring extra decimal points to represent"""
+	
+	# Default config
+	config.pvalue_min_dps = 2
+	config.pvalue_max_dps = 3
+	config.pvalue_leading_zero = True
+	config.alpha = 0.05
+	
+	assert fmt_p(0.009, html=False) == '= 0.009*'
+
+def test_fmt_pvalues_ambiguous():
+	"""Test formatting of p values requiring extra decimal points to avoid ambiguity"""
+	
+	# Default config
+	config.pvalue_min_dps = 2
+	config.pvalue_max_dps = 3
+	config.pvalue_leading_zero = True
+	config.alpha = 0.05
+	
+	assert fmt_p(0.048, html=False) == '= 0.048*'
+	assert fmt_p(0.052, html=False) == '= 0.052'
+	
+	# Special rounding rules
+	assert fmt_p(0.04999, html=False) == '= 0.049*'
+	assert fmt_p(0.05001, html=False) == '= 0.051'
+
+def test_fmt_pvalues_extreme():
+	"""Test formatting of p values too small or large to be represented"""
+	
+	# Default config
+	config.pvalue_min_dps = 2
+	config.pvalue_max_dps = 3
+	config.pvalue_leading_zero = True
+	config.alpha = 0.05
+	
+	assert fmt_p(0.0009, html=False) == '< 0.001*'
+	assert fmt_p(0.999, html=False) == '> 0.99'

yli/__init__.py

@@ -15,6 +15,7 @@
 #   along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 from .bayes_factors import bayesfactor_afbf
+from .config import config
 from .distributions import beta_oddsratio, beta_ratio, hdi, transformed_dist
 from .io import pickle_read_compressed, pickle_read_encrypted, pickle_write_compressed, pickle_write_encrypted
 from .regress import PenalisedLogit, regress, vif

yli/config.py

@@ -0,0 +1,32 @@
+#   scipy-yli: Helpful SciPy utilities and recipes
+#   Copyright © 2022  Lee Yingtong Li (RunasSudo)
+#
+#   This program is free software: you can redistribute it and/or modify
+#   it under the terms of the GNU Affero General Public License as published by
+#   the Free Software Foundation, either version 3 of the License, or
+#   (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU Affero General Public License for more details.
+#
+#   You should have received a copy of the GNU Affero General Public License
+#   along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+class Config:
+	"""Stores global configuration for the library"""
+	
+	def __init__(self):
+		# Display at least this many decimal places for p values
+		self.pvalue_min_dps = 2
+		# Display at most this many decimal places for p values
+		self.pvalue_max_dps = 3
+		# Display a leading zero for p values
+		self.pvalue_leading_zero = True
+		
+		# Alpha level for significance tests, confidence intervals
+		self.alpha = 0.05
+
+"""Global config singleton"""
+config = Config()

yli/utils.py

@@ -20,6 +20,8 @@ import patsy
 
 import warnings
 
+from .config import config
+
 # ----------------------------
 # Data cleaning and validation
 
@@ -63,25 +65,47 @@ def as_2groups(df, data, group):
 def do_fmt_p(p):
 	"""Return sign and formatted p value"""
 	
-	if p < 0.001:
+	if p < 10**-config.pvalue_max_dps:
-		return '<', '0.001*'
+		# Smaller than min value
-	elif p < 0.0095:
+		return '<', '{:.1g}'.format(10**-config.pvalue_max_dps)
-		return None, '{:.3f}*'.format(p)
+	
-	elif p < 0.045:
+	if p > 1 - 10**-config.pvalue_min_dps:
-		return None, '{:.2f}*'.format(p)
+		# Larger than max value
-	elif p < 0.05:
+		return '>', '{0:.{dps}f}'.format(1 - 10**-config.pvalue_min_dps, dps=config.pvalue_min_dps)
-		return None, '{:.3f}*'.format(p)  # 3dps to show significance
+	
-	elif p < 0.055:
+	if round(p, config.pvalue_min_dps) == config.alpha:
-		return None, '{:.3f}'.format(p)   # 3dps to show non-significance
+		# Rounding to pvalue_min_dps makes significance ambiguous
-	elif p < 0.095:
+		
-		return None, '{:.2f}'.format(p)
+		if round(p, config.pvalue_max_dps) == config.alpha:
-	else:
+			# Still ambiguous to pvalue_max_dps
-		return None, '{:.1f}'.format(p)
+			
+			if p < config.alpha:
+				# Significant: round down
+				p = config.alpha - 10**-config.pvalue_max_dps
+			else:
+				# Nonsignificant: round up
+				p = config.alpha + 10**-config.pvalue_max_dps
+		
+		return None, '{0:.{dps}f}'.format(p, dps=config.pvalue_max_dps)
+	
+	if p < 10**-config.pvalue_min_dps:
+		# Insufficient resolution at pvalue_min_dps
+		# We know from earlier comparison that 1 s.f. fits within pvalue_max_dps
+		return None, '{:.1g}'.format(p)
+	
+	# OK to round to pvalue_min_dps
+	return None, '{0:.{dps}f}'.format(p, dps=config.pvalue_min_dps)
 
 def fmt_p(p, *, html, nospace=False):
 	"""Format p value"""
 	
 	sign, fmt = do_fmt_p(p)
+	
+	if not config.pvalue_leading_zero:
+		fmt = fmt.lstrip('0')
+	if p < config.alpha:
+		fmt += '*'
+	
 	if sign is not None:
 		if nospace:
 			pfmt = sign + fmt  # e.g. "<0.001"