Skip to content

Commit 005b6ac

Browse files
committed
When there are 0 flu tests, subtype percent positivity should be null
1 parent 9f00620 commit 005b6ac

3 files changed

Lines changed: 8 additions & 4 deletions

File tree

src/acquisition/rvdss/pull_historic.py

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -300,6 +300,10 @@ def create_percent_positive_detection_table(table,modified_date,start_year, flu=
300300

301301
table["flu_positive_tests"] = table["flua_positive_tests"] + table["flub_positive_tests"]
302302
table["flu_pct_positive"] = (table["flu_positive_tests"]/table["flu_tests"])*100
303+
304+
table.loc[table["flu_tests"] == 0,"flua_pct_positive"] = np.nan
305+
table.loc[table["flu_tests"] == 0,"flub_pct_positive"] = np.nan
306+
303307
else:
304308
table[virus+"_positive_tests"] = (table[virus+"_pct_positive"]/100) *table[virus+"_tests"]
305309

testdata/acquisition/rvdss/formatted_flu_positive_tests.csv

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,12 +2,12 @@ epiweek,time_value,issue,geo_type,geo_value,flua_pct_positive,flub_pct_positive,
22
201635,2016-09-03,2017-01-25,nation,ca,0.11,0,1862,2.0482,0,2.0482,0.11
33
201635,2016-09-03,2017-01-25,region,atlantic,0,0,79,0,0,0,0
44
201635,2016-09-03,2017-01-25,province,qc,0,0,431,0,0,0,0
5-
201635,2016-09-03,2017-01-25,province,on,0.18,0,568,1.0224,0,1.0224,0.18
5+
201635,2016-09-03,2017-01-25,province,on,NA,NA,0,0,0,0,NA
66
201635,2016-09-03,2017-01-25,region,prairies,0.16,0,616,0.9856,0,0.9856,0.16
77
201635,2016-09-03,2017-01-25,province,bc,0,0,151,0,0,0,0
88
201635,2016-09-03,2017-01-25,region,territories,0,0,17,0,0,0,0
99
201636,2016-09-10,2017-01-25,nation,ca,0.49,0.55,1630,7.986999999999999,8.965000000000002,16.952,1.04
10-
201636,2016-09-10,2017-01-25,region,atlantic,0,0,55,0,0,0,0
10+
201636,2016-09-10,2017-01-25,region,atlantic,NA,NA,0,0,0,0,NA
1111
201636,2016-09-10,2017-01-25,province,qc,0.25,0,400,1,0,1,0.25
1212
201636,2016-09-10,2017-01-25,province,on,0.21,0.62,481,1.0101,2.9821999999999997,3.9923,0.83
1313
201636,2016-09-10,2017-01-25,region,prairies,0.18,0.7,571,1.0278,3.997,5.0248,0.88

testdata/acquisition/rvdss/week3_20162017.html

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -14875,7 +14875,7 @@
1487514875
<p class="p1"><span class="s1"></span><br></p>
1487614876
</td>
1487714877
<td valign="middle" class="td2">
14878-
<p class="p2"><span class="s1">&lt;td&gt;568&lt;/td&gt;</span></p>
14878+
<p class="p2"><span class="s1">&lt;td&gt;0&lt;/td&gt;</span></p>
1487914879
</td>
1488014880
</tr>
1488114881
<tr>
@@ -15027,7 +15027,7 @@
1502715027
<p class="p1"><span class="s1"></span><br></p>
1502815028
</td>
1502915029
<td valign="middle" class="td2">
15030-
<p class="p2"><span class="s1">&lt;td&gt;55&lt;/td&gt;</span></p>
15030+
<p class="p2"><span class="s1">&lt;td&gt;0&lt;/td&gt;</span></p>
1503115031
</td>
1503215032
</tr>
1503315033
<tr>

0 commit comments

Comments
 (0)