diff --git a/.Rhistory b/.Rhistory new file mode 100644 index 000000000..e69de29bb diff --git a/Unpublished/NEW-RULE/negative/01/data/.env b/Unpublished/NEW-RULE/negative/01/data/.env new file mode 100644 index 000000000..665776c69 --- /dev/null +++ b/Unpublished/NEW-RULE/negative/01/data/.env @@ -0,0 +1,3 @@ +PRODUCT=SDTMIG +VERSION=3-4 + diff --git a/Unpublished/NEW-RULE/negative/01/data/_datasets.csv b/Unpublished/NEW-RULE/negative/01/data/_datasets.csv new file mode 100644 index 000000000..6b18b7361 --- /dev/null +++ b/Unpublished/NEW-RULE/negative/01/data/_datasets.csv @@ -0,0 +1,3 @@ +Filename,Label +cm,Concomitant/Prior Medications +mh,Medical History \ No newline at end of file diff --git a/Unpublished/NEW-RULE/negative/01/data/_variables.csv b/Unpublished/NEW-RULE/negative/01/data/_variables.csv new file mode 100644 index 000000000..07cb6c75b --- /dev/null +++ b/Unpublished/NEW-RULE/negative/01/data/_variables.csv @@ -0,0 +1,30 @@ +dataset,variable,label,type,length +cm,STUDYID,Study Identifier,Char,12 +cm,DOMAIN,Domain Abbreviation,Char,2 +cm,USUBJID,Unique Subject Identifier,Char,8 +cm,CMSEQ,Sequence Number,Num,8 +cm,CMTRT,"Reported Name of Drug, Med, or Therapy",Char,200 +cm,CMINDC,Indication,Char,200 +cm,CMDOSE,Dose per Administration,Num,8 +cm,CMDOSU,Dose Units,Char,6 +cm,CMDOSFRQ,Dosing Frequency per Interval,Char,3 +cm,CMROUTE,Route of Administration,Char,24 +cm,EPOCH,Epoch,Char,9 +cm,CMSTDTC,Start Date/Time of Medication,Char,10 +cm,CMENDTC,End Date/Time of Medication,Char,10 +cm,CMSTDY,Study Day of Start of Medication,Num,8 +cm,CMENDY,Study Day of End of Medication,Num,8 +cm,CMENRTPT,End Relative to Reference Time Point,Char,7 +cm,CMENTPT,End Reference Time Point,Char,10 +mh,STUDYID,Study Identifier,Char,12 +mh,DOMAIN,Domain Abbreviation,Char,2 +mh,USUBJID,Unique Subject Identifier,Char,8 +mh,MHSEQ,Sequence Number,Num,8 +mh,MHTERM,Reported Term for the Medical History,Char,19 +mh,MHEVDTYP,Medical History Event Date Type,Char,13 +mh,MHSTDTC,Start Date/Time of Medical History Event,Char,10 +mh,MHSTDY,Study Day of Start of Observation,Num,8 +mh,MHENDTC,End Date/Time of Medical History Event,Char,50 +mh,MHENDY,Study Day of End of Observation,Num,8 +mh,MHENRTPT,End Relative to Reference Time Point,Char,50 +mh,MHENTPT,End Reference Time Point,Char,50 \ No newline at end of file diff --git a/Unpublished/NEW-RULE/negative/01/data/cm.csv b/Unpublished/NEW-RULE/negative/01/data/cm.csv new file mode 100644 index 000000000..29bb46793 --- /dev/null +++ b/Unpublished/NEW-RULE/negative/01/data/cm.csv @@ -0,0 +1,6 @@ +STUDYID,DOMAIN,USUBJID,CMSEQ,CMTRT,CMINDC,CMDOSE,CMDOSU,CMDOSFRQ,CMROUTE,EPOCH,CMSTDTC,CMENDTC,CMSTDY,CMENDY,CMENRTPT,CMENTPT +CDISCPILOT01,CM,CDISC005,1,CENTRUM SILVER,PROPHYLAXIS OR NON-THERAPEUTIC USE,1,TABLET,,ORAL,SCREENING,2012-03,,,,,2013-08-06 +CDISCPILOT01,CM,CDISC005,4,HYDROCORTISONE,PROPHYLAXIS OR NON-THERAPEUTIC USE,1,TABLET,,TOPICAL,TREATMENT,2013-05-14,,100,,,2013-08-06 +CDISCPILOT01,CM,CDISC017,1,ACETAMINOPHEN,PROPHYLAXIS OR NON-THERAPEUTIC USE,2,TABLET,,ORAL,SCREENING,2008,,,,,2014-03-08 +CDISCPILOT01,CM,CDISC017,2,MULTIVITAMIN,PROPHYLAXIS OR NON-THERAPEUTIC USE,1,TABLET,,ORAL,SCREENING,2011-08,,,,,2014-03-08 +CDISCPILOT01,CM,CDISC017,3,VITAMIN E,PROPHYLAXIS OR NON-THERAPEUTIC USE,400,mg,,ORAL,SCREENING,2011-08,,,,,2014-03-08 diff --git a/Unpublished/NEW-RULE/negative/01/data/mh.csv b/Unpublished/NEW-RULE/negative/01/data/mh.csv new file mode 100644 index 000000000..70a8d00d8 --- /dev/null +++ b/Unpublished/NEW-RULE/negative/01/data/mh.csv @@ -0,0 +1,5 @@ +STUDYID,DOMAIN,USUBJID,MHSEQ,MHTERM,MHEVDTYP,MHSTDTC,MHSTDY,MHENDTC,MHENDY,MHENRTPT,MHENTPT +CDISCPILOT01,MH,CDISC001,1,ALZHEIMER'S DISEASE,SYMPTOM ONSET,2004-05-28,-3108,,,,2021-05-01 +CDISCPILOT01,MH,CDISC002,1,ALZHEIMER'S DISEASE,SYMPTOM ONSET,2010-03-19,-972,2010-03-21,-970,,2021-02-15 +CDISCPILOT01,MH,CDISC003,1,ALZHEIMER'S DISEASE,SYMPTOM ONSET,2007-02-09,-2393,2007-02-09,-2393,,2015-05-09 +CDISCPILOT01,MH,CDISC004,1,ALZHEIMER'S DISEASE,SYMPTOM ONSET,2010-11-05,-1068,,,,2011-06-11 diff --git a/Unpublished/NEW-RULE/negative/01/results/results.csv b/Unpublished/NEW-RULE/negative/01/results/results.csv new file mode 100644 index 000000000..c062782c7 --- /dev/null +++ b/Unpublished/NEW-RULE/negative/01/results/results.csv @@ -0,0 +1 @@ +Dataset,Record,Variable,Value diff --git a/Unpublished/NEW-RULE/positive/01/data/.env b/Unpublished/NEW-RULE/positive/01/data/.env new file mode 100644 index 000000000..929573120 --- /dev/null +++ b/Unpublished/NEW-RULE/positive/01/data/.env @@ -0,0 +1,2 @@ +PRODUCT=SDTMIG +VERSION=3-4 \ No newline at end of file diff --git a/Unpublished/NEW-RULE/positive/01/data/_datasets.csv b/Unpublished/NEW-RULE/positive/01/data/_datasets.csv new file mode 100644 index 000000000..6b18b7361 --- /dev/null +++ b/Unpublished/NEW-RULE/positive/01/data/_datasets.csv @@ -0,0 +1,3 @@ +Filename,Label +cm,Concomitant/Prior Medications +mh,Medical History \ No newline at end of file diff --git a/Unpublished/NEW-RULE/positive/01/data/_variables.csv b/Unpublished/NEW-RULE/positive/01/data/_variables.csv new file mode 100644 index 000000000..07cb6c75b --- /dev/null +++ b/Unpublished/NEW-RULE/positive/01/data/_variables.csv @@ -0,0 +1,30 @@ +dataset,variable,label,type,length +cm,STUDYID,Study Identifier,Char,12 +cm,DOMAIN,Domain Abbreviation,Char,2 +cm,USUBJID,Unique Subject Identifier,Char,8 +cm,CMSEQ,Sequence Number,Num,8 +cm,CMTRT,"Reported Name of Drug, Med, or Therapy",Char,200 +cm,CMINDC,Indication,Char,200 +cm,CMDOSE,Dose per Administration,Num,8 +cm,CMDOSU,Dose Units,Char,6 +cm,CMDOSFRQ,Dosing Frequency per Interval,Char,3 +cm,CMROUTE,Route of Administration,Char,24 +cm,EPOCH,Epoch,Char,9 +cm,CMSTDTC,Start Date/Time of Medication,Char,10 +cm,CMENDTC,End Date/Time of Medication,Char,10 +cm,CMSTDY,Study Day of Start of Medication,Num,8 +cm,CMENDY,Study Day of End of Medication,Num,8 +cm,CMENRTPT,End Relative to Reference Time Point,Char,7 +cm,CMENTPT,End Reference Time Point,Char,10 +mh,STUDYID,Study Identifier,Char,12 +mh,DOMAIN,Domain Abbreviation,Char,2 +mh,USUBJID,Unique Subject Identifier,Char,8 +mh,MHSEQ,Sequence Number,Num,8 +mh,MHTERM,Reported Term for the Medical History,Char,19 +mh,MHEVDTYP,Medical History Event Date Type,Char,13 +mh,MHSTDTC,Start Date/Time of Medical History Event,Char,10 +mh,MHSTDY,Study Day of Start of Observation,Num,8 +mh,MHENDTC,End Date/Time of Medical History Event,Char,50 +mh,MHENDY,Study Day of End of Observation,Num,8 +mh,MHENRTPT,End Relative to Reference Time Point,Char,50 +mh,MHENTPT,End Reference Time Point,Char,50 \ No newline at end of file diff --git a/Unpublished/NEW-RULE/positive/01/data/cm.csv b/Unpublished/NEW-RULE/positive/01/data/cm.csv new file mode 100644 index 000000000..38a953a35 --- /dev/null +++ b/Unpublished/NEW-RULE/positive/01/data/cm.csv @@ -0,0 +1,7 @@ +STUDYID,DOMAIN,USUBJID,CMSEQ,CMTRT,CMINDC,CMDOSE,CMDOSU,CMDOSFRQ,CMROUTE,EPOCH,CMSTDTC,CMENDTC,CMSTDY,CMENDY,CMENRTPT,CMENTPT +CDISCPILOT01,CM,CDISC004,1,VITAMIN C,PROPHYLAXIS OR NON-THERAPEUTIC USE,500,mg,,ORAL,SCREENING,1983,,,,ONGOING,2014-03-18 +CDISCPILOT01,CM,CDISC004,2,VITAMIN E,PROPHYLAXIS OR NON-THERAPEUTIC USE,400,mg,,ORAL,SCREENING,1983,,,,ONGOING,2014-03-18 +CDISCPILOT01,CM,CDISC007,1,METAMUCIL,PROPHYLAXIS OR NON-THERAPEUTIC USE,3,mg,,ORAL,SCREENING,2009,,,,ONGOING,2013-06-20 +CDISCPILOT01,CM,CDISC007,2,ADVIL,PROPHYLAXIS OR NON-THERAPEUTIC USE,200,mg,,ORAL,SCREENING,2011,,,,ONGOING,2013-06-20 +CDISCPILOT01,CM,CDISC007,3,DOCUSATE SODIUM,PROPHYLAXIS OR NON-THERAPEUTIC USE,100,mg,,ORAL,SCREENING,2012-11,2013-01-05,,1,, +CDISCPILOT01,CM,CDISC007,4,BENADRYL,PROPHYLAXIS OR NON-THERAPEUTIC USE,75,mg,,ORAL,SCREENING,2013-02-18,2013-05-10,45,126,ONGOING, diff --git a/Unpublished/NEW-RULE/positive/01/data/mh.csv b/Unpublished/NEW-RULE/positive/01/data/mh.csv new file mode 100644 index 000000000..99494d53c --- /dev/null +++ b/Unpublished/NEW-RULE/positive/01/data/mh.csv @@ -0,0 +1,5 @@ +STUDYID,DOMAIN,USUBJID,MHSEQ,MHTERM,MHEVDTYP,MHSTDTC,MHSTDY,MHENDTC,MHENDY,MHENRTPT,MHENTPT +CDISCPILOT01,MH,CDISC009,1,ALZHEIMER'S DISEASE,SYMPTOM ONSET,2008-09-02,-1511,,,ONGOING,2021-05-04 +CDISCPILOT01,MH,CDISC010,1,ALZHEIMER'S DISEASE,SYMPTOM ONSET,2012-09-08,-378,,,ONGOING,2021-05-05 +CDISCPILOT01,MH,CDISC011,1,ALZHEIMER'S DISEASE,SYMPTOM ONSET,2002-12-01,-3659,,,ONGOING,2021-05-06 +CDISCPILOT01,MH,CDISC012,1,ALZHEIMER'S DISEASE,SYMPTOM ONSET,2009-03-16,-1632,,,, diff --git a/Unpublished/NEW-RULE/positive/01/results/results.csv b/Unpublished/NEW-RULE/positive/01/results/results.csv new file mode 100644 index 000000000..c062782c7 --- /dev/null +++ b/Unpublished/NEW-RULE/positive/01/results/results.csv @@ -0,0 +1 @@ +Dataset,Record,Variable,Value diff --git a/Unpublished/NEW-RULE/rule.yml b/Unpublished/NEW-RULE/rule.yml new file mode 100644 index 000000000..a6411f440 --- /dev/null +++ b/Unpublished/NEW-RULE/rule.yml @@ -0,0 +1,75 @@ +Authorities: + - Organization: CDISC + Standards: + - Name: SDTMIG + References: + - Citations: + - Cited Guidance: The description or date and/or time of a time point that acts as + a fixed reference for characterizing the end of an + observation. This is the sponsor-defined reference point + referred to by --ENRTPT. + Document: Model v2.0 + Item: --ENTPT + Section: Timing + Origin: SDTM and SDTMIG Conformance Rules + Rule Identifier: + Id: CG0045 + Version: '1' + Version: '2.0' + Version: '3.4' + - Name: SDTMIG + References: + - Citations: + - Cited Guidance: Identifies the end of the observation as being before or after + the sponsor-defined reference time point defined by variable + --ENTPT. + Document: Model v1.7 + Item: Table 2.2.5.1 --ENTPT + Section: 2.2.5 Timing Variables for All Classes + Origin: SDTM and SDTMIG Conformance Rules + Rule Identifier: + Id: CG0045 + Version: '1' + Version: '2.0' + Version: '3.3' + - Name: SDTMIG + References: + - Citations: + - Cited Guidance: (--ENRTPT) Identifies the end of the observation as being before + or after the sponsor-defined reference time point defined by + variable --ENTPT. + Document: Model v1.4 + Item: Specification + Section: 2.2.5 Timing Variables for All Classes + Origin: SDTM and SDTMIG Conformance Rules + Rule Identifier: + Id: CG0045 + Version: '1' + Version: '2.0' + Version: '3.2' +Check: + all: + - operator: 'non_empty' + name: '--ENTPT' + - operator: 'empty' + name: '--ENRTPT' +Core: + Id: '' + Status: Draft + Version: '1' +Description: 'Raise an error when --ENTPT is populated and --ENRTPT is not populated.' +Executability: Fully Executable +Outcome: + Message: '--ENTPT is populated, but --ENRTPT is not populated.' + Output Variables: + - '--ENTPT' + - '--ENRTPT' +Rule Type: 'Record Data' +Scope: + Classes: + Include: + - ALL + Domains: + Include: + - ALL +Sensitivity: 'Record' diff --git a/setup/bash_setup.sh b/setup/bash_setup.sh old mode 100644 new mode 100755