Merge pull request #8 from rileyhazard/child.prediction.changes

Child prediction changes
ihmeuw · Nov 30, 2020 · 38595f4 · 38595f4
2 parents d2b4b79 + b920e62
commit 38595f4
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diff --git a/docs/changelog_v2.1.md b/docs/changelog_v2.1.md
@@ -0,0 +1,6 @@
+# Changelog 2.1
+
+* Reduce the threshold for child undetermined causes of death (PR8)
+* Remove the majority of child sepsis spurious symptoms (PR8)
+* Amend the child homicide rule (PR8)
+
diff --git a/pkg/smartva.xml b/pkg/smartva.xml
@@ -1,7 +1,7 @@
 <project>
     <shortName>SmartVA</shortName>
     <fullName>SmartVA-Analyze</fullName>
-    <version>2.0.0</version>
+    <version>2.1.0</version>
     <componentList>
         <component>
             <name>default</name>

diff --git a/smartva/__init__.py b/smartva/__init__.py
@@ -1,2 +1,2 @@
 prog_name = 'SmartVA-Analyze'
-version = '2.0.0'
+version = '2.1.0'
diff --git a/smartva/data/child_tariff_data.py b/smartva/data/child_tariff_data.py
@@ -10,7 +10,7 @@
 
 CUTOFF_POS = 0.95
 
-UNIFORM_LIST_POS = 0.24
+UNIFORM_LIST_POS = 0.30
 
 MIN_CAUSE_SCORE = defaultdict(lambda: 3.7)
 
@@ -161,28 +161,9 @@
         's99992',  # word_accid
     ],
     20: [  # Sepsis
-        's999924',  # word_icu
-        's2991',  # quintile 1 of age
-        's999923',  # word_heart
-        's999911',  # word_cold
         's999929',  # word_lung
-        's13991',  # decedent was small or very small
-        's999947',  # word_swell
         's999933',  # word_pneumonia
-        's2992',  # quintile 2 of age
-        's164',  # Decedent did not suffer accident
-        's14',  # What was the weight of the deceased at birth?
-        's188',  # Has the deceased's (biological) mother ever been tested for HIV?
         's99998',  # word_breath
-        's125',  # During the illness that led to death, did [name] have difficult breathing?
-        's117',  # How many days before death did the frequent loose or liquid stools start? [days]
-        's28',  # How old was the baby/child when the fatal illness started? [days]
-        's31',  # How old was the deceased at the time of death? [days]
-        's2994',  # quintile 4 of age
-        's2995',  # quintile 5 of age
-        's17',  # Did the baby ever cry?
-        's18',  # Did the baby ever move?
-        's19',  # Did the baby ever breathe?
     ],
     21: [  # Homicide
         's153',

diff --git a/smartva/data/constants.py b/smartva/data/constants.py
@@ -102,6 +102,7 @@ class Child(object):
     POISONING = 'c4_47_4'
     BITE = 'c4_47_5'
     BURN = 'c4_47_6'
+    VIOLENCE = 'c4_47_7'
     NO_INJURY = 'c4_47_11'
     OTHER_INJURY = 'c4_47_8a'
     INFLICTED_BY_OTHER = 'c4_48'

diff --git a/smartva/res/about.html b/smartva/res/about.html
@@ -46,7 +46,7 @@
 			<b>Version</b>
 		</p>
 		<p>
-			Smart VA 2.0.0
+			Smart VA 2.1.0
 		</p>
 	</body>
 </html>
diff --git a/smartva/res/documentation.docx b/smartva/res/documentation.docx
diff --git a/smartva/res/documentation.fld/image001.png b/smartva/res/documentation.fld/image001.png
diff --git a/smartva/res/documentation.fld/props002.xml b/smartva/res/documentation.fld/props002.xml
@@ -1,2 +1,2 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<ds:datastoreItem ds:itemID="{806B25D1-F386-8948-990F-B5D5661F0C46}" xmlns:ds="http://schemas.openxmlformats.org/officeDocument/2006/customXml"><ds:schemaRefs><ds:schemaRef ds:uri="http://schemas.openxmlformats.org/officeDocument/2006/bibliography"/></ds:schemaRefs></ds:datastoreItem>
+<ds:datastoreItem ds:itemID="{5D289D1F-7A34-7548-B6F4-B4959FB4C47F}" xmlns:ds="http://schemas.openxmlformats.org/officeDocument/2006/customXml"><ds:schemaRefs><ds:schemaRef ds:uri="http://schemas.openxmlformats.org/officeDocument/2006/bibliography"/></ds:schemaRefs></ds:datastoreItem>
diff --git a/smartva/res/documentation.html b/smartva/res/documentation.html
diff --git a/smartva/rules/homicide_child.py b/smartva/rules/homicide_child.py
@@ -8,8 +8,10 @@
 def logic_rule(row):
     value_of = value_from_row(row, int_or_float)
 
-    injury_by_other = value_of(Child.INFLICTED_BY_OTHER) == YES
-
+    injury_by_other = any([
+        value_of(Child.INFLICTED_BY_OTHER) == YES,
+        value_of(Child.VIOLENCE) == YES,
+    ])
     recent = value_of(Child.INJURY_DAYS) < INJURY_DURATION_CUTTOFF
 
     no_unintentional_injury = all([

diff --git a/test/tariff_prep/child-predictions.csv b/test/tariff_prep/child-predictions.csv
@@ -125,7 +125,7 @@ sid,cause,cause34,age,sex
 124,,Undetermined,1,1
 125,,Undetermined,1,1
 126,,Undetermined,1,1
-127,,Undetermined,1,1
+127,1,AIDS,1,1
 128,,Undetermined,1,1
 129,,Undetermined,1,1
 130,,Undetermined,1,1
@@ -183,7 +183,7 @@ sid,cause,cause34,age,sex
 182,,Undetermined,1,1
 183,3,Diarrhea/Dysentery,1,1
 184,8,Hemorrhagic fever,1,1
-185,,Undetermined,1,1
+185,3,Diarrhea/Dysentery,1,1
 186,,Undetermined,1,1
 187,,Undetermined,1,1
 188,,Undetermined,1,1