reverting to unique carton counts

assets/positivity_tally.tsv

@@ -1,21 +1 @@
-Processing Plant State	Total Cartons	Negative Cartons	Positive Cartons	Latest Date Sampled
-CA	1	1	0	2024-05-20
-CO	24	10	14	2024-10-07
-FL	1	1	0	2024-05-20
-IA	10	10	0	2024-07-30
-ID	1	1	0	2024-05-20
-IL	3	3	0	2024-06-17
-IN	6	5	1	2024-07-02
-KS	2	2	0	2024-07-02
-KY	6	3	3	2024-07-02
-MI	31	5	26	2024-10-07
-MN	6	6	0	2024-07-02
-MO	4	2	2	2024-09-10
-NC	2	2	0	2024-09-24
-NY	6	4	2	2024-09-24
-OH	5	5	0	2024-07-28
-OR	1	1	0	2024-05-20
-TX	3	1	2	2024-06-05
-UT	1	1	0	2024-05-02
-VA	2	2	0	2024-07-02
-WI	104	93	11	2024-10-07
+

scripts/positivity_tally.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3
 
 """
-This script processes detection results for HPAI (Highly Pathogenic Avian Influenza) and generates a summary report.
+This script processes detection results for HPAI (Highly Pathogenic Avian Influenza)
+and generates a summary report.
 
 Usage:
     python positivity_tally.py <input_file> <output_file>
@@ -20,9 +21,9 @@
 Output:
     The script will generate a TSV file with the following columns:
     - Processing Plant State: State where the processing plant is located
-    - Total Cartons: Total number of cartons tested
-    - Positive Cartons: Number of cartons that tested positive for HPAI
-    - Negative Cartons: Number of cartons that tested negative for HPAI
+    - Total Cartons: Total number of unique cartons tested
+    - Positive Cartons: Number of unique cartons that tested positive for HPAI
+    - Negative Cartons: Number of unique cartons that tested negative for HPAI
     - Latest Date Sampled: Most recent date when samples were taken for each state
 
 Required libraries:
@@ -64,7 +65,7 @@ def tally_all_cartons(detections: pl.LazyFrame) -> pl.LazyFrame:
     """
     Tally all cartons in the detection results.
 
-    This function counts the total number of cartons for each processing plant state.
+    This function counts the total number of unique cartons for each processing plant state.
 
     Args:
         detections (pl.LazyFrame): A LazyFrame containing the detection results.
@@ -75,7 +76,7 @@ def tally_all_cartons(detections: pl.LazyFrame) -> pl.LazyFrame:
     return (
         detections.select("Processing Plant State", "carton")
         .group_by("Processing Plant State")
-        .len()
+        .n_unique()
         .rename({"len": "Total Cartons"})
     )
 
@@ -85,7 +86,7 @@ def count_positive_detections(detections: pl.LazyFrame) -> pl.LazyFrame:
     Count the number of positive HPAI detections for each processing plant state.
 
     This function filters the detections for positive HPAI results,
-    counts the number of positive cartons for each state, and renames
+    counts the number of unique positive cartons for each state, and renames
     the resulting column.
 
     Args:
@@ -98,7 +99,7 @@ def count_positive_detections(detections: pl.LazyFrame) -> pl.LazyFrame:
         detections.filter(pl.col("positive_for_HPAI").eq(True))  # noqa: FBT003
         .select("Processing Plant State", "carton")
         .group_by("Processing Plant State")
-        .len()  # this should be changed to `.n_unique()` for unique cartons only
+        .n_unique()  # this should be changed to `.n_unique()` for unique cartons only
         .rename({"len": "Positive Cartons"})
     )
 
@@ -108,7 +109,7 @@ def count_negative_detections(detections: pl.LazyFrame) -> pl.LazyFrame:
     Count the number of negative HPAI detections for each processing plant state.
 
     This function filters the detections for negative HPAI results,
-    counts the number of negative cartons for each state, and renames
+    counts the number of unique negative cartons for each state, and renames
     the resulting column.
 
     Args:
@@ -121,7 +122,7 @@ def count_negative_detections(detections: pl.LazyFrame) -> pl.LazyFrame:
         detections.filter(pl.col("positive_for_HPAI").eq(False))  # noqa: FBT003
         .select("Processing Plant State", "carton")
         .group_by("Processing Plant State")
-        .len()  # this should be changed to `.n_unique()` for unique cartons only
+        .n_unique()  # this should be changed to `.n_unique()` for unique cartons only
         .rename({"len": "Negative Cartons"})
     )