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Merge pull request #237 from pharmaverse/236-missing-csv-mb_ms_be
Closes #236: Add CSV for MB, MS, BE
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‎inst/extdata/be.csv‎

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"STUDYID","DOMAIN","USUBJID","BESEQ","BEREFID","BELNKID","BETERM","BECAT","BELOC","VISITNUM","BEDTC","BESTDTC","BEENDTC"
2+
"CDISCPILOT01","BE","01-701-1015",1,"SPEC1.1",NA,"Specimen Collection","COLLECTION","SKIN OF THE AXILLA",1,"2025-06-14T08:00","2025-06-14T08:00",NA
3+
"CDISCPILOT01","BE","01-701-1015",2,"ALIQ1.1.1",NA,"Aliquoting","PREPARATION","SKIN OF THE AXILLA",1,"2025-06-14T08:00","2025-06-14T09:00",NA
4+
"CDISCPILOT01","BE","01-701-1015",3,"ALIQ1.1.2",NA,"Aliquoting","PREPARATION","SKIN OF THE AXILLA",1,"2025-06-14T08:00","2025-06-15T09:30",NA
5+
"CDISCPILOT01","BE","01-701-1015",4,"ALIQ1.1.2-C",NA,"Culturing","CULTURE","SKIN OF THE AXILLA",1,"2025-06-14T08:00","2025-06-15T10:00","2025-06-30T10:00"
6+
"CDISCPILOT01","BE","01-701-1015",5,"ALIQ1.1.3",NA,"Aliquoting","PREPARATION","SKIN OF THE AXILLA",1,"2025-06-14T08:00","2025-06-15T09:45",NA
7+
"CDISCPILOT01","BE","01-701-1015",6,"ALIQ1.1.3-C",NA,"Culturing","CULTURE","SKIN OF THE AXILLA",1,"2025-06-14T08:00","2025-06-15T11:00","2025-06-30T11:00"
8+
"CDISCPILOT01","BE","01-701-1015",7,"SPEC1.2",NA,"Specimen Collection","COLLECTION","SKIN OF THE AXILLA",2,"2025-06-21T08:00","2025-06-21T08:00",NA
9+
"CDISCPILOT01","BE","01-701-1015",8,"ALIQ1.2.1",NA,"Aliquoting","PREPARATION","SKIN OF THE AXILLA",2,"2025-06-21T08:00","2025-06-22T09:30",NA
10+
"CDISCPILOT01","BE","01-701-1015",9,"ALIQ1.2.1-C",NA,"Culturing","CULTURE","SKIN OF THE AXILLA",2,"2025-06-21T08:00","2025-06-22T10:00","2025-07-07T10:00"
11+
"CDISCPILOT01","BE","01-701-1023",1,"SPEC2.1",NA,"Specimen Collection","COLLECTION","URINARY SYSTEM",1,"2025-07-15T08:00","2025-07-15T08:00",NA
12+
"CDISCPILOT01","BE","01-701-1023",2,"ALIQ2.1.1",NA,"Aliquoting","PREPARATION","URINARY SYSTEM",1,"2025-07-15T08:00","2025-07-15T09:30",NA
13+
"CDISCPILOT01","BE","01-701-1023",3,"ALIQ2.1.2",NA,"Aliquoting","PREPARATION","URINARY SYSTEM",1,"2025-07-15T08:00","2025-07-16T09:30",NA
14+
"CDISCPILOT01","BE","01-701-1023",4,"ALIQ2.1.2-C",NA,"Culturing","CULTURE","URINARY SYSTEM",1,"2025-07-15T08:00","2025-07-16T10:00","2025-07-31T10:00"
15+
"CDISCPILOT01","BE","01-701-1023",5,"SPEC2.2",NA,"Specimen Collection","COLLECTION","URINARY SYSTEM",2,"2025-07-22T08:00","2025-07-22T08:00",NA
16+
"CDISCPILOT01","BE","01-701-1023",6,"ALIQ2.2.1",NA,"Aliquoting","PREPARATION","URINARY SYSTEM",2,"2025-07-22T08:00","2025-07-23T09:30",NA
17+
"CDISCPILOT01","BE","01-701-1023",7,"ALIQ2.2.1-C",NA,"Culturing","CULTURE","URINARY SYSTEM",2,"2025-07-22T08:00","2025-07-23T10:00","2025-08-07T10:00"
18+
"CDISCPILOT01","BE","01-701-1028",1,"SPEC3.1",NA,"Specimen Collection","COLLECTION","SKIN OF THE AXILLA",1,"2025-08-11T08:00","2025-08-11T08:00",NA
19+
"CDISCPILOT01","BE","01-701-1028",2,"ALIQ3.1.1",NA,"Aliquoting","PREPARATION","SKIN OF THE AXILLA",1,"2025-08-11T08:00","2025-08-12T09:30",NA
20+
"CDISCPILOT01","BE","01-701-1028",3,"ALIQ3.1.1-C",NA,"Culturing","CULTURE","SKIN OF THE AXILLA",1,"2025-08-11T08:00","2025-08-12T10:00","2025-08-27T10:00"
21+
"CDISCPILOT01","BE","01-701-1028",4,"ALIQ3.1.2",NA,"Aliquoting","PREPARATION","SKIN OF THE AXILLA",1,"2025-08-11T08:00","2025-08-30T09:30",NA
22+
"CDISCPILOT01","BE","01-701-1028",5,"ALIQ3.1.2-C",NA,"Culturing","CULTURE","SKIN OF THE AXILLA",1,"2025-08-11T08:00","2025-08-30T10:00","2025-09-14T10:00"
23+
"CDISCPILOT01","BE","01-701-1033",1,"SPEC4.1",NA,"Specimen Collection","COLLECTION","LUNG",1,"2025-09-10T08:00","2025-09-10T08:00",NA
24+
"CDISCPILOT01","BE","01-701-1033",2,"ALIQ4.1.1",NA,"Aliquoting","PREPARATION","LUNG",1,"2025-09-10T08:00","2025-09-11T09:30",NA
25+
"CDISCPILOT01","BE","01-701-1033",3,"ALIQ4.1.1-C",NA,"Culturing","CULTURE","LUNG",1,"2025-09-10T08:00","2025-09-11T10:00","2025-09-26T10:00"
26+
"CDISCPILOT01","BE","01-701-1034",1,"SPEC5.1",NA,"Specimen Collection","COLLECTION","LUNG",1,"2025-10-05T08:00","2025-10-05T08:00",NA
27+
"CDISCPILOT01","BE","01-701-1034",2,"ALIQ5.1.1",NA,"Aliquoting","PREPARATION","LUNG",1,"2025-10-05T08:00","2025-10-05T09:30",NA
28+
"CDISCPILOT01","BE","01-701-1034",3,"ALIQ5.1.1-C",NA,"Culturing","CULTURE","LUNG",1,"2025-10-05T08:00","2025-10-05T10:00","2025-10-20T10:00"
29+
"CDISCPILOT01","BE","01-701-1034",4,"ALIQ5.1.2",NA,"Aliquoting","PREPARATION","LUNG",1,"2025-10-05T08:00","2025-10-05T09:45",NA
30+
"CDISCPILOT01","BE","01-701-1034",5,"ALIQ5.1.2-C",NA,"Culturing","CULTURE","LUNG",1,"2025-10-05T08:00","2025-10-05T11:00","2025-10-20T11:00"
31+
"CDISCPILOT01","BE","01-701-1034",6,"SPEC5.2",NA,"Specimen Collection","COLLECTION","LUNG",2,"2025-10-15T08:00","2025-10-15T08:00",NA
32+
"CDISCPILOT01","BE","01-701-1034",7,"ALIQ5.2.1",NA,"Aliquoting","PREPARATION","LUNG",2,"2025-10-15T08:00","2025-10-16T09:30",NA
33+
"CDISCPILOT01","BE","01-701-1034",8,"ALIQ5.2.1-C",NA,"Culturing","CULTURE","LUNG",2,"2025-10-15T08:00","2025-10-16T10:00","2025-10-31T10:00"
34+
"CDISCPILOT01","BE","01-701-1034",9,"ALIQ5.2.2",NA,"Aliquoting","PREPARATION","LUNG",2,"2025-10-15T08:00","2025-10-16T09:45",NA
35+
"CDISCPILOT01","BE","01-701-1034",10,"ALIQ5.2.2-C",NA,"Culturing","CULTURE","LUNG",2,"2025-10-15T08:00","2025-10-16T11:00","2025-10-31T11:00"
36+
"CDISCPILOT01","BE","01-701-1047",1,"SPEC6.1",NA,"Specimen Collection","COLLECTION","LUNG",1,"2025-11-01T08:00","2025-11-01T08:00",NA
37+
"CDISCPILOT01","BE","01-701-1047",2,"ALIQ6.1.1",NA,"Aliquoting","PREPARATION","LUNG",1,"2025-11-01T08:00","2025-11-01T09:30",NA
38+
"CDISCPILOT01","BE","01-701-1047",3,"ALIQ6.1.1-C",NA,"Culturing","CULTURE","LUNG",1,"2025-11-01T08:00","2025-11-01T10:00","2025-11-16T10:00"
39+
"CDISCPILOT01","BE","01-701-1047",4,"ALIQ6.1.2",NA,"Aliquoting","PREPARATION","LUNG",1,"2025-11-01T08:00","2025-11-01T09:30",NA
40+
"CDISCPILOT01","BE","01-701-1047",5,"ALIQ6.1.2-C",NA,"Culturing","CULTURE","LUNG",1,"2025-11-01T08:00","2025-11-01T10:00","2025-11-16T10:00"
41+
"CDISCPILOT01","BE","01-701-1057",1,"SPEC7.1",NA,"Specimen Collection","COLLECTION","STOMACH",1,"2025-12-01T08:00","2025-12-01T08:00",NA
42+
"CDISCPILOT01","BE","01-701-1057",2,"ALIQ7.1.1",NA,"Aliquoting","PREPARATION","STOMACH",1,"2025-12-01T08:00","2025-12-01T09:30",NA
43+
"CDISCPILOT01","BE","01-701-1057",3,"ALIQ7.1.1",NA,"Aliquoting","PREPARATION","STOMACH",1,"2025-12-01T08:00","2025-12-02T09:30",NA
44+
"CDISCPILOT01","BE","01-701-1057",4,"ALIQ7.1.1-C",NA,"Culturing","CULTURE","STOMACH",1,"2025-12-01T08:00","2025-12-02T10:00","2025-12-17T10:00"

‎inst/extdata/mb.csv‎

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"STUDYID","DOMAIN","USUBJID","MBSEQ","MBGRPID","MBREFID","MBLNKGRP","MBTESTCD","MBTEST","MBTSTDTL","MBORRES","MBORRESU","MBRSLSCL","MBSTRESC","MBSTRESN","MBSTRESU","MBSPEC","MBLOC","MBMETHOD","VISITNUM","MBDTC"
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"CDISCPILOT01","MB","01-701-1015",1,1,"ALIQ1.1.2","ALIQ1.1.2-C","GMNCOC","Gram Negative Cocci","DETECTION","PRESENT",NA,"Ord","PRESENT",NA,NA,"SKIN TISSUE","SKIN OF THE AXILLA","GRAM STAIN",1,"2025-06-14T08:00"
3+
"CDISCPILOT01","MB","01-701-1015",2,1,"ALIQ1.1.2","ALIQ1.1.2-C","GMNCOC","Gram Negative Cocci","QUANTIFICATION","2+",NA,"Ord","2+","2",NA,"SKIN TISSUE","SKIN OF THE AXILLA","GRAM STAIN",1,"2025-06-14T08:00"
4+
"CDISCPILOT01","MB","01-701-1015",3,2,"ALIQ1.1.2","ALIQ1.1.2-C","MCCOLCNT","Colony Count","QUANTIFICATION","100","CFU/mL","Quant","100","CFU/mL","CFU/mL","SKIN TISSUE","SKIN OF THE AXILLA","COLONY COUNT",1,"2025-06-14T08:00"
5+
"CDISCPILOT01","MB","01-701-1015",4,3,"ALIQ1.1.3","ALIQ1.1.3-C","GNROD","Gram Negative Rods","DETECTION","PRESENT",NA,"Ord","PRESENT",NA,NA,"SKIN TISSUE","SKIN OF THE AXILLA","GRAM STAIN",1,"2025-06-14T08:00"
6+
"CDISCPILOT01","MB","01-701-1015",5,3,"ALIQ1.1.3","ALIQ1.1.3-C","GNROD","Gram Negative Rods","QUANTIFICATION","1+",NA,"Ord","1+","1",NA,"SKIN TISSUE","SKIN OF THE AXILLA","GRAM STAIN",1,"2025-06-14T08:00"
7+
"CDISCPILOT01","MB","01-701-1015",6,4,"ALIQ1.1.3","ALIQ1.1.3-C","MCCOLCNT","Colony Count","QUANTIFICATION","50","CFU/mL","Quant","50","CFU/mL","CFU/mL","SKIN TISSUE","SKIN OF THE AXILLA","COLONY COUNT",1,"2025-06-14T08:00"
8+
"CDISCPILOT01","MB","01-701-1015",7,5,"ALIQ1.2.1","ALIQ1.2.1-C","GNROD","Gram Negative Rods","DETECTION","PRESENT",NA,"Ord","PRESENT",NA,NA,"SKIN TISSUE","SKIN OF THE AXILLA","GRAM STAIN",2,"2025-06-21T08:00"
9+
"CDISCPILOT01","MB","01-701-1015",8,5,"ALIQ1.2.1","ALIQ1.2.1-C","GNROD","Gram Negative Rods","QUANTIFICATION","3+",NA,"Ord","3+","3",NA,"SKIN TISSUE","SKIN OF THE AXILLA","GRAM STAIN",2,"2025-06-21T08:00"
10+
"CDISCPILOT01","MB","01-701-1015",9,6,"ALIQ1.2.1","ALIQ1.2.1-C","MCCOLCNT","Colony Count","QUANTIFICATION","500","CFU/mL","Quant","500","CFU/mL","CFU/mL","SKIN TISSUE","SKIN OF THE AXILLA","COLONY COUNT",2,"2025-06-21T08:00"
11+
"CDISCPILOT01","MB","01-701-1023",1,1,"ALIQ2.1.2","ALIQ2.1.2-C","GPRCOC","Gram Positive Cocci","DETECTION","PRESENT",NA,"Ord","PRESENT",NA,NA,"URINE","URINARY SYSTEM","GRAM STAIN",1,"2025-07-15T08:00"
12+
"CDISCPILOT01","MB","01-701-1023",2,1,"ALIQ2.1.2","ALIQ2.1.2-C","GPRCOC","Gram Positive Cocci","QUANTIFICATION","4+",NA,"Ord","4+","4",NA,"URINE","URINARY SYSTEM","GRAM STAIN",1,"2025-07-15T08:00"
13+
"CDISCPILOT01","MB","01-701-1023",3,2,"ALIQ2.1.2","ALIQ2.1.2-C","MCCOLCNT","Colony Count","QUANTIFICATION","300","CFU/mL","Quant","300","CFU/mL","CFU/mL","URINE","URINARY SYSTEM","COLONY COUNT",1,"2025-07-15T08:00"
14+
"CDISCPILOT01","MB","01-701-1033",1,1,"ALIQ4.1.1","ALIQ4.1.1-C","GPRCOC","Gram Positive Cocci","DETECTION","PRESENT",NA,"Ord","PRESENT",NA,NA,"SPUTUM","LUNG","GRAM STAIN",1,"2025-09-10T08:00"
15+
"CDISCPILOT01","MB","01-701-1033",2,1,"ALIQ4.1.1","ALIQ4.1.1-C","GPRCOC","Gram Positive Cocci","QUANTIFICATION","2+",NA,"Ord","2+","2",NA,"SPUTUM","LUNG","GRAM STAIN",1,"2025-09-10T08:00"
16+
"CDISCPILOT01","MB","01-701-1033",3,2,"ALIQ4.1.1","ALIQ4.1.1-C","MCCOLCNT","Colony Count","QUANTIFICATION","150","CFU/mL","Quant","150","CFU/mL","CFU/mL","SPUTUM","LUNG","COLONY COUNT",1,"2025-09-10T08:00"
17+
"CDISCPILOT01","MB","01-701-1047",1,1,"ALIQ6.1.1","ALIQ6.1.1-C","MCORGIDN","Microbial Organism Identification","RESULT","NO GROWTH",NA,"Nom","NO GROWTH",NA,NA,"SPUTUM","LUNG","MICROBIAL CULTURE, SOLID",1,"2025-11-01T08:00"
18+
"CDISCPILOT01","MB","01-701-1047",2,2,"ALIQ6.1.2","ALIQ6.1.2-C","MCORGIDN","Microbial Organism Identification","RESULT","NO GROWTH",NA,"Nom","NO GROWTH",NA,NA,"SPUTUM","LUNG","MICROBIAL CULTURE, SOLID",1,"2025-11-01T08:00"
19+
"CDISCPILOT01","MB","01-701-1057",1,1,"ALIQ7.1.1","ALIQ7.1.1-C","MTBCMPLX","Mycobacterium tuberculosis complex","DETECTION","PRESENT",NA,"Ord","PRESENT",NA,NA,"LAVAGE FLUID","STOMACH","NUCLEIC ACID AMPLIFICATION TEST",1,"2025-12-01T08:00"

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