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calculate total positive flu types from positive subtype tests
1 parent 005b6ac commit b52c78a

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Lines changed: 47 additions & 43 deletions

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‎src/acquisition/rvdss/pull_historic.py‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -232,9 +232,13 @@ def create_detections_table(table,modified_date,week_number,week_end_date,start_
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'geo_type':geo_types})
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table.columns =[re.sub(" ","_",col) for col in table.columns]
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# calculate total flu positive tests from a and b positive tests
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if "flua_positive_tests" in table.columns and "flub_positive_tests" in table.columns:
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table["flu_positive_tests"] = table["flua_positive_tests"] + table["flub_positive_tests"]
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return(table)
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def create_percent_positive_detection_table(table,modified_date,start_year, flu=False,overwrite_weeks=False):
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table = deduplicate_rows(table)
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table.columns = [re.sub(' +', ' ',col) for col in table.columns]

‎testdata/acquisition/rvdss/formatted_detections.csv‎

Lines changed: 42 additions & 42 deletions
Original file line numberDiff line numberDiff line change
@@ -1,42 +1,42 @@
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epiweek,time_value,issue,geo_type,geo_value,flu_tests,fluah1n1pdm09_positive_tests,fluah3_positive_tests,fluauns_positive_tests,flua_positive_tests,flub_positive_tests,rsv_tests,rsv_positive_tests,hpiv_tests,hpiv1_positive_tests,hpiv2_positive_tests,hpiv3_positive_tests,hpiv4_positive_tests,hpivother_positive_tests,adv_tests,adv_positive_tests,hmpv_tests,hmpv_positive_tests,evrv_tests,evrv_positive_tests,hcov_tests,hcov_positive_tests
2-
201703,2017-01-21,2017-01-25,province,nl,87,0,4,4,8,0,87,7,87,0,1,1,0,0,87,0,87,3,87,1,NA,NA
3-
201703,2017-01-21,2017-01-25,province,pe,58,0,17,0,17,0,58,6,2,0,0,0,0,0,2,0,2,0,2,0,2,1
4-
201703,2017-01-21,2017-01-25,province,ns,119,0,0,12,12,0,109,18,20,0,0,1,0,0,20,0,20,0,20,1,20,7
5-
201703,2017-01-21,2017-01-25,province,nb,247,0,0,43,43,0,249,33,57,0,0,1,0,0,57,2,57,1,57,5,57,7
6-
201703,2017-01-21,2017-01-25,region,atlantic,511,0,21,59,80,0,503,64,166,0,1,3,0,0,166,2,166,4,166,7,79,15
7-
201703,2017-01-21,2017-01-25,lab,région nord est,330,0,0,18,18,0,293,62,0,0,0,0,0,0,0,0,0,0,NA,NA,0,0
8-
201703,2017-01-21,2017-01-25,lab,québec chaudière appalaches,608,0,0,93,93,2,380,83,139,0,0,5,0,0,140,2,108,0,NA,NA,108,0
9-
201703,2017-01-21,2017-01-25,lab,centre du québec,659,0,49,102,151,4,490,118,0,0,0,0,0,0,0,0,0,0,NA,NA,0,0
10-
201703,2017-01-21,2017-01-25,lab,montréal laval,1653,0,0,300,300,6,1101,167,632,1,2,3,3,0,644,24,613,28,NA,NA,549,27
11-
201703,2017-01-21,2017-01-25,lab,ouest du québec,403,0,0,75,75,2,147,33,0,0,0,0,0,0,0,0,0,0,NA,NA,0,0
12-
201703,2017-01-21,2017-01-25,lab,montérégie,342,0,0,69,69,1,285,49,0,0,0,0,0,0,0,0,0,0,NA,NA,0,0
13-
201703,2017-01-21,2017-01-25,province,qc,3995,0,49,657,706,15,2696,512,771,1,2,8,3,0,784,26,721,28,NA,NA,657,27
14-
201703,2017-01-21,2017-01-25,lab,ottawa phl,64,0,14,0,14,0,64,7,64,0,0,1,0,0,64,0,64,9,64,1,64,16
15-
201703,2017-01-21,2017-01-25,lab,cheo ottawa,304,0,0,42,42,0,304,60,29,0,0,0,0,0,29,0,51,3,29,1,29,2
16-
201703,2017-01-21,2017-01-25,lab,kingston phl,76,0,17,0,17,0,76,11,76,1,4,2,0,0,76,1,74,4,76,3,74,11
17-
201703,2017-01-21,2017-01-25,lab,uhn mount sinai hospital,433,0,0,71,71,0,433,24,18,0,0,0,0,0,0,0,18,0,0,0,0,0
18-
201703,2017-01-21,2017-01-25,lab,cphl toronto,1559,2,613,1,616,3,1174,102,1174,0,2,7,2,0,1174,9,1169,36,1174,28,1169,98
19-
201703,2017-01-21,2017-01-25,lab,sick kids hospital toronto,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
20-
201703,2017-01-21,2017-01-25,lab,sunnybrook womens college hsc,127,0,12,10,22,0,127,10,127,0,1,1,0,0,127,0,127,4,127,1,127,12
21-
201703,2017-01-21,2017-01-25,lab,sault ste marie phl,24,0,4,0,4,0,24,5,24,0,0,2,0,0,24,0,24,1,24,0,24,3
22-
201703,2017-01-21,2017-01-25,lab,timmins phl,14,0,1,0,1,0,14,3,14,0,0,1,0,0,14,0,14,1,14,1,14,2
23-
201703,2017-01-21,2017-01-25,lab,st josephs london,100,0,0,16,16,0,100,6,18,0,1,0,0,0,0,0,18,2,0,0,0,0
24-
201703,2017-01-21,2017-01-25,lab,london phl,399,2,100,2,104,1,399,65,399,0,2,8,4,0,399,6,397,17,399,13,397,57
25-
201703,2017-01-21,2017-01-25,lab,orillia phl,228,0,38,0,38,0,227,42,227,0,1,3,1,0,227,5,226,8,227,15,226,22
26-
201703,2017-01-21,2017-01-25,lab,thunder bay phl,36,0,7,0,7,0,32,6,32,0,0,0,0,0,32,0,32,1,32,2,32,6
27-
201703,2017-01-21,2017-01-25,lab,sudbury phl,62,0,7,0,7,0,62,6,62,0,0,1,0,0,62,0,60,0,62,4,60,5
28-
201703,2017-01-21,2017-01-25,lab,hamilton phl,201,1,54,2,57,3,190,32,190,0,0,2,0,0,190,3,186,6,190,13,186,17
29-
201703,2017-01-21,2017-01-25,lab,peterborough phl,139,0,31,1,32,0,139,21,139,0,0,4,0,0,139,0,139,3,139,9,139,9
30-
201703,2017-01-21,2017-01-25,province,on,3766,5,898,145,1048,7,3365,400,2593,1,11,32,7,0,2557,24,2599,95,2557,91,2541,260
31-
201703,2017-01-21,2017-01-25,province,mb,333,0,7,11,18,0,331,92,55,0,0,1,0,0,55,0,44,2,55,1,44,11
32-
201703,2017-01-21,2017-01-25,lab,regina,536,0,101,10,111,0,536,113,536,0,0,13,3,0,536,9,536,7,536,28,536,50
33-
201703,2017-01-21,2017-01-25,lab,saskatoon,217,0,0,32,32,1,217,40,37,0,0,1,0,0,37,1,37,0,37,2,37,0
34-
201703,2017-01-21,2017-01-25,province,sk,753,0,101,42,143,1,753,153,573,0,0,14,3,0,573,10,573,7,573,30,573,50
35-
201703,2017-01-21,2017-01-25,province,ab,1336,0,202,48,250,4,1336,185,1336,33,0,0,0,0,1336,9,1336,10,1336,30,1336,30
36-
201703,2017-01-21,2017-01-25,region,prairies,2422,0,310,101,411,5,2420,430,1964,33,0,15,3,0,1964,19,1953,19,1964,61,1953,91
37-
201703,2017-01-21,2017-01-25,province,bc,1360,0,55,362,417,20,1360,149,277,2,3,11,6,0,277,2,277,22,277,30,277,27
38-
201703,2017-01-21,2017-01-25,province,yt,27,0,2,4,6,0,27,7,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
39-
201703,2017-01-21,2017-01-25,province,nt,32,0,7,1,8,0,32,6,32,1,0,0,0,0,32,1,32,0,32,1,32,3
40-
201703,2017-01-21,2017-01-25,province,nu,44,0,8,6,14,0,44,2,44,0,3,0,0,0,44,2,44,0,44,16,44,4
41-
201703,2017-01-21,2017-01-25,region,territories,103,0,17,11,28,0,103,15,76,1,3,0,0,0,76,3,76,0,76,17,76,7
42-
201703,2017-01-21,2017-01-25,nation,ca,12157,5,1350,1335,2690,47,10447,1570,5847,38,20,69,19,0,5824,76,5792,168,5040,206,5583,427
1+
epiweek,time_value,issue,geo_type,geo_value,flu_tests,fluah1n1pdm09_positive_tests,fluah3_positive_tests,fluauns_positive_tests,flua_positive_tests,flub_positive_tests,rsv_tests,rsv_positive_tests,hpiv_tests,hpiv1_positive_tests,hpiv2_positive_tests,hpiv3_positive_tests,hpiv4_positive_tests,hpivother_positive_tests,adv_tests,adv_positive_tests,hmpv_tests,hmpv_positive_tests,evrv_tests,evrv_positive_tests,hcov_tests,hcov_positive_tests,flu_positive_tests
2+
201703,2017-01-21,2017-01-25,province,nl,87,0,4,4,8,0,87,7,87,0,1,1,0,0,87,0,87,3,87,1,NA,NA,8
3+
201703,2017-01-21,2017-01-25,province,pe,58,0,17,0,17,0,58,6,2,0,0,0,0,0,2,0,2,0,2,0,2,1,17
4+
201703,2017-01-21,2017-01-25,province,ns,119,0,0,12,12,0,109,18,20,0,0,1,0,0,20,0,20,0,20,1,20,7,12
5+
201703,2017-01-21,2017-01-25,province,nb,247,0,0,43,43,0,249,33,57,0,0,1,0,0,57,2,57,1,57,5,57,7,43
6+
201703,2017-01-21,2017-01-25,region,atlantic,511,0,21,59,80,0,503,64,166,0,1,3,0,0,166,2,166,4,166,7,79,15,80
7+
201703,2017-01-21,2017-01-25,lab,région nord est,330,0,0,18,18,0,293,62,0,0,0,0,0,0,0,0,0,0,NA,NA,0,0,18
8+
201703,2017-01-21,2017-01-25,lab,québec chaudière appalaches,608,0,0,93,93,2,380,83,139,0,0,5,0,0,140,2,108,0,NA,NA,108,0,95
9+
201703,2017-01-21,2017-01-25,lab,centre du québec,659,0,49,102,151,4,490,118,0,0,0,0,0,0,0,0,0,0,NA,NA,0,0,155
10+
201703,2017-01-21,2017-01-25,lab,montréal laval,1653,0,0,300,300,6,1101,167,632,1,2,3,3,0,644,24,613,28,NA,NA,549,27,306
11+
201703,2017-01-21,2017-01-25,lab,ouest du québec,403,0,0,75,75,2,147,33,0,0,0,0,0,0,0,0,0,0,NA,NA,0,0,77
12+
201703,2017-01-21,2017-01-25,lab,montérégie,342,0,0,69,69,1,285,49,0,0,0,0,0,0,0,0,0,0,NA,NA,0,0,70
13+
201703,2017-01-21,2017-01-25,province,qc,3995,0,49,657,706,15,2696,512,771,1,2,8,3,0,784,26,721,28,NA,NA,657,27,721
14+
201703,2017-01-21,2017-01-25,lab,ottawa phl,64,0,14,0,14,0,64,7,64,0,0,1,0,0,64,0,64,9,64,1,64,16,14
15+
201703,2017-01-21,2017-01-25,lab,cheo ottawa,304,0,0,42,42,0,304,60,29,0,0,0,0,0,29,0,51,3,29,1,29,2,42
16+
201703,2017-01-21,2017-01-25,lab,kingston phl,76,0,17,0,17,0,76,11,76,1,4,2,0,0,76,1,74,4,76,3,74,11,17
17+
201703,2017-01-21,2017-01-25,lab,uhn mount sinai hospital,433,0,0,71,71,0,433,24,18,0,0,0,0,0,0,0,18,0,0,0,0,0,71
18+
201703,2017-01-21,2017-01-25,lab,cphl toronto,1559,2,613,1,616,3,1174,102,1174,0,2,7,2,0,1174,9,1169,36,1174,28,1169,98,619
19+
201703,2017-01-21,2017-01-25,lab,sick kids hospital toronto,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
20+
201703,2017-01-21,2017-01-25,lab,sunnybrook womens college hsc,127,0,12,10,22,0,127,10,127,0,1,1,0,0,127,0,127,4,127,1,127,12,22
21+
201703,2017-01-21,2017-01-25,lab,sault ste marie phl,24,0,4,0,4,0,24,5,24,0,0,2,0,0,24,0,24,1,24,0,24,3,4
22+
201703,2017-01-21,2017-01-25,lab,timmins phl,14,0,1,0,1,0,14,3,14,0,0,1,0,0,14,0,14,1,14,1,14,2,1
23+
201703,2017-01-21,2017-01-25,lab,st josephs london,100,0,0,16,16,0,100,6,18,0,1,0,0,0,0,0,18,2,0,0,0,0,16
24+
201703,2017-01-21,2017-01-25,lab,london phl,399,2,100,2,104,1,399,65,399,0,2,8,4,0,399,6,397,17,399,13,397,57,105
25+
201703,2017-01-21,2017-01-25,lab,orillia phl,228,0,38,0,38,0,227,42,227,0,1,3,1,0,227,5,226,8,227,15,226,22,38
26+
201703,2017-01-21,2017-01-25,lab,thunder bay phl,36,0,7,0,7,0,32,6,32,0,0,0,0,0,32,0,32,1,32,2,32,6,7
27+
201703,2017-01-21,2017-01-25,lab,sudbury phl,62,0,7,0,7,0,62,6,62,0,0,1,0,0,62,0,60,0,62,4,60,5,7
28+
201703,2017-01-21,2017-01-25,lab,hamilton phl,201,1,54,2,57,3,190,32,190,0,0,2,0,0,190,3,186,6,190,13,186,17,60
29+
201703,2017-01-21,2017-01-25,lab,peterborough phl,139,0,31,1,32,0,139,21,139,0,0,4,0,0,139,0,139,3,139,9,139,9,32
30+
201703,2017-01-21,2017-01-25,province,on,3766,5,898,145,1048,7,3365,400,2593,1,11,32,7,0,2557,24,2599,95,2557,91,2541,260,1055
31+
201703,2017-01-21,2017-01-25,province,mb,333,0,7,11,18,0,331,92,55,0,0,1,0,0,55,0,44,2,55,1,44,11,18
32+
201703,2017-01-21,2017-01-25,lab,regina,536,0,101,10,111,0,536,113,536,0,0,13,3,0,536,9,536,7,536,28,536,50,111
33+
201703,2017-01-21,2017-01-25,lab,saskatoon,217,0,0,32,32,1,217,40,37,0,0,1,0,0,37,1,37,0,37,2,37,0,33
34+
201703,2017-01-21,2017-01-25,province,sk,753,0,101,42,143,1,753,153,573,0,0,14,3,0,573,10,573,7,573,30,573,50,144
35+
201703,2017-01-21,2017-01-25,province,ab,1336,0,202,48,250,4,1336,185,1336,33,0,0,0,0,1336,9,1336,10,1336,30,1336,30,254
36+
201703,2017-01-21,2017-01-25,region,prairies,2422,0,310,101,411,5,2420,430,1964,33,0,15,3,0,1964,19,1953,19,1964,61,1953,91,416
37+
201703,2017-01-21,2017-01-25,province,bc,1360,0,55,362,417,20,1360,149,277,2,3,11,6,0,277,2,277,22,277,30,277,27,437
38+
201703,2017-01-21,2017-01-25,province,yt,27,0,2,4,6,0,27,7,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,6
39+
201703,2017-01-21,2017-01-25,province,nt,32,0,7,1,8,0,32,6,32,1,0,0,0,0,32,1,32,0,32,1,32,3,8
40+
201703,2017-01-21,2017-01-25,province,nu,44,0,8,6,14,0,44,2,44,0,3,0,0,0,44,2,44,0,44,16,44,4,14
41+
201703,2017-01-21,2017-01-25,region,territories,103,0,17,11,28,0,103,15,76,1,3,0,0,0,76,3,76,0,76,17,76,7,28
42+
201703,2017-01-21,2017-01-25,nation,ca,12157,5,1350,1335,2690,47,10447,1570,5847,38,20,69,19,0,5824,76,5792,168,5040,206,5583,427,2737

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