Merge pull request #1011 from adilraza99/GH1010-skip-ci-when-nobs-zero

jonbrenas · web-flow · commit 5e74b9f7e9e6 · 2026-03-04T09:27:33.000Z
fix: return NaN confidence intervals when cohort size is zero
diff --git a/malariagen_data/anoph/frq_base.py b/malariagen_data/anoph/frq_base.py
@@ -140,6 +140,9 @@ def _add_frequency_ci(*, ds, ci_method):
             frq_ci_low, frq_ci_upp = proportion_confint(
                 count=count, nobs=nobs, method=ci_method
             )
+        loc_zero = nobs == 0
+        frq_ci_low[loc_zero] = np.nan
+        frq_ci_upp[loc_zero] = np.nan
         ds["event_frequency_ci_low"] = ("variants", "cohorts"), frq_ci_low
         ds["event_frequency_ci_upp"] = ("variants", "cohorts"), frq_ci_upp
 

Original file line number	Diff line number	Diff line change
`@@ -140,6 +140,9 @@ def _add_frequency_ci(*, ds, ci_method):`
`140`	`140`	`frq_ci_low, frq_ci_upp = proportion_confint(`
`141`	`141`	`count=count, nobs=nobs, method=ci_method`
`142`	`142`	`)`
	`143`	`+ loc_zero = nobs == 0`
	`144`	`+ frq_ci_low[loc_zero] = np.nan`
	`145`	`+ frq_ci_upp[loc_zero] = np.nan`
`143`	`146`	`ds["event_frequency_ci_low"] = ("variants", "cohorts"), frq_ci_low`
`144`	`147`	`ds["event_frequency_ci_upp"] = ("variants", "cohorts"), frq_ci_upp`
`145`	`148`