Specify which methods have correction vs none

czbiohub-sf · Nov 25, 2024 · 690ba3a · 690ba3a
1 parent d3ae7d1
commit 690ba3a
Show file tree

Hide file tree

Showing 3 changed files with 11 additions and 7 deletions.
diff --git a/README.md b/README.md
@@ -45,13 +45,13 @@ class_counts = np.array([
     200, # misc
 ])
 
-# Get parasitemia only
+# Compute parasitemia without correction
 parasitemia = corrector.calc_parasitemia(class_counts)
 
-# Get parasitemia and 95% confidence bounds as parasites/uL
+# Get corrected parasitemia and 95% confidence bounds as parasites/uL
 parasitemia, conf_bounds = corrector.get_res_from_counts(class_counts, units_ul_out=True)
 
-# Get parasitemia and 95% confidence bounds as percentage
+# Get corrected parasitemia and 95% confidence bounds as percentage
 parasitemia, conf_bounds = corrector.get_res_from_counts(class_counts, units_ul_out=False)
 ```
 

diff --git a/stats_utils/compensator.py b/stats_utils/compensator.py
@@ -160,7 +160,8 @@ def _reformat_7x1_to_2x1(self, counts: npt.NDArray) -> npt.NDArray:
 
     def calc_parasitemia(self, counts: npt.NDArray) -> float:
         """
-        Wrapper for base class method _calc_parasitemia()
+        Wrapper for base class method _calc_parasitemia(), computes parasitemia
+        without compensation
 
         Reformats 7x1 array into required 2x1 array before computing statistics
 
@@ -176,7 +177,8 @@ def get_res_from_counts(
         self, raw_counts: npt.NDArray, units_ul_out: bool = False
     ) -> Tuple[float, float]:
         """
-        Wrapper for base class method _get_res_from_counts()
+        Wrapper for base class method _get_res_from_counts(), returns compensated
+        parasitemia and corresponding 95% confidence bounds
 
         Reformats 7x1 array into required 2x1 array before computing statistics
 

diff --git a/stats_utils/deskewer.py b/stats_utils/deskewer.py
@@ -70,7 +70,8 @@ def __init__(self, model_name: str):
 
     def calc_parasitemia(self, counts: npt.NDArray) -> float:
         """
-        Wrapper for base class method _calc_parasitemia()
+        Wrapper for base class method _calc_parasitemia(), computes parasitemia
+        without deskewing
 
         Input(s)
         - counts:
@@ -83,7 +84,8 @@ def get_res_from_counts(
         self, raw_counts: npt.NDArray, units_ul_out: bool = False
     ) -> Tuple[float, float]:
         """
-        Wrapper for base class method _get_res_from_counts()
+        Wrapper for base class method _get_res_from_counts(), returns deskewed
+        parasitemia and corresponding 95% confidence bounds
 
         Input(s)
         - counts: