From 8a9f6d994326934623e8e6278ba9f1f03587349b Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Wed, 1 May 2024 14:34:51 +0000 Subject: [PATCH] cli-40502-625 --- 404.html | 8 +- LICENSE-text.html | 8 +- LICENSE.html | 8 +- articles/Building_Specification_Readers.html | 388 +++++++++---------- articles/Example.html | 14 +- articles/index.html | 8 +- authors.html | 25 +- index.html | 9 +- news/index.html | 19 +- pkgdown.yml | 6 +- reference/MetaCore_filter.html | 8 +- reference/check_columns.html | 8 +- reference/check_structure.html | 8 +- reference/check_words.html | 8 +- reference/checks.html | 8 +- reference/create_tbl.html | 8 +- reference/define_to_MetaCore.html | 8 +- reference/get_control_term.html | 48 +-- reference/get_keys.html | 121 ++++++ reference/index.html | 12 +- reference/is_metacore.html | 8 +- reference/load_metacore.html | 8 +- reference/metacore.html | 8 +- reference/metacore_example.html | 8 +- reference/pipe.html | 8 +- reference/read_all_sheets.html | 8 +- reference/save_metacore.html | 8 +- reference/select_dataset.html | 8 +- reference/spec_to_metacore.html | 16 +- reference/spec_type.html | 8 +- reference/spec_type_to_codelist.html | 8 +- reference/spec_type_to_derivations.html | 8 +- reference/spec_type_to_ds_spec.html | 8 +- reference/spec_type_to_ds_vars.html | 8 +- reference/spec_type_to_value_spec.html | 8 +- reference/spec_type_to_var_spec.html | 8 +- reference/xml_to_codelist.html | 8 +- reference/xml_to_derivations.html | 8 +- reference/xml_to_ds_spec.html | 8 +- reference/xml_to_ds_vars.html | 8 +- reference/xml_to_value_spec.html | 8 +- reference/xml_to_var_spec.html | 8 +- sitemap.xml | 3 + 43 files changed, 514 insertions(+), 403 deletions(-) create mode 100644 reference/get_keys.html diff --git a/404.html b/404.html index 91b98ab..4e873f4 100644 --- a/404.html +++ b/404.html @@ -6,7 +6,7 @@ Page not found (404) • metacore - + @@ -34,7 +34,7 @@ metacore - 0.1.2 + 0.1.3 @@ -100,12 +100,12 @@

Page not found (404)

diff --git a/LICENSE-text.html b/LICENSE-text.html index 012c6b4..f59b9cc 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -1,5 +1,5 @@ -License • metacoreLicense • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -74,11 +74,11 @@

License

diff --git a/LICENSE.html b/LICENSE.html index 35594f9..96bdaee 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -1,5 +1,5 @@ -MIT License • metacoreMIT License • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -78,11 +78,11 @@

MIT License

diff --git a/articles/Building_Specification_Readers.html b/articles/Building_Specification_Readers.html index 0797c82..9eaba9a 100644 --- a/articles/Building_Specification_Readers.html +++ b/articles/Building_Specification_Readers.html @@ -6,7 +6,7 @@ Building Specification Readers • metacore - + @@ -35,7 +35,7 @@ metacore - 0.1.2 + 0.1.3 @@ -434,12 +434,12 @@

Building Specification Readers

#> # A tibble: 6 × 8 #> dataset variable origin type code_id derivation_id where sig_dig #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <int> -#> 1 ADAE STUDYID Predecessor Text NA NA TRUE NA -#> 2 ADAE USUBJID Predecessor Text NA NA TRUE NA -#> 3 ADAE SUBJID Predecessor Text NA NA TRUE NA -#> 4 ADAE SITEID Predecessor Text NA NA TRUE NA -#> 5 ADAE AGE Predecessor Integer NA NA TRUE NA -#> 6 ADAE SEX Predecessor Text SEX NA TRUE NA +#> 1 ADAE STUDYID Predecessor Text NA pred.NA TRUE NA +#> 2 ADAE USUBJID Predecessor Text NA pred.NA TRUE NA +#> 3 ADAE SUBJID Predecessor Text NA pred.NA TRUE NA +#> 4 ADAE SITEID Predecessor Text NA pred.NA TRUE NA +#> 5 ADAE AGE Predecessor Integer NA pred.NA TRUE NA +#> 6 ADAE SEX Predecessor Text SEX pred.NA TRUE NA

The derivation table is relatively simple by comparison. It just has two columns, the derivation id and the derivation. But, the derivation comes from the supplied derivation, predecessor, or comment column @@ -549,190 +549,190 @@

Building Specification Readers

#> ATM #> ADTM #> Warning: The following derivations are never used: -#> AE.STUDYID: AE.STUDYID -#> AE.USUBJID: AE.USUBJID -#> AE.SUBJID: AE.SUBJID -#> ADSL.SITEID: ADSL.SITEID -#> ADSL.AGE: ADSL.AGE -#> ADSL.SEX: ADSL.SEX -#> ADSL.RACE: ADSL.RACE -#> ADSL.ACOUNTRY: ADSL.ACOUNTRY -#> ADSL.FASFL: ADSL.FASFL -#> ADSL.ITTFL: ADSL.ITTFL -#> ADSL.SAFFL: ADSL.SAFFL -#> ADSL.PPROTFL: ADSL.PPROTFL -#> ADSL.TRTxxPN that corresponds to the treatment selected in TRTP: ADSL.TRTxxPN that corresponds to the treatment selected in TRTP -#> ADSL.TRTxxAN that corresponds to the treatment selected in TRTA: ADSL.TRTxxAN that corresponds to the treatment selected in TRTA -#> ADSL.TRT01A: ADSL.TRT01A -#> ADSL.TRT01AN: ADSL.TRT01AN -#> ADSL.TRT01P: ADSL.TRT01P -#> ADSL.TRT01PN: ADSL.TRT01PN -#> ADSL.TRTSEQP: ADSL.TRTSEQP -#> ADSL.TRTSEQPN: ADSL.TRTSEQPN -#> ADSL.TRTSEQA: ADSL.TRTSEQA -#> ADSL.TRTSEQAN: ADSL.TRTSEQAN -#> AE.AESTDY: AE.AESTDY -#> AE.AESTDTC: AE.AESTDTC -#> AE.AEENDTC: AE.AEENDTC -#> AE.AEENDY: AE.AEENDY -#> AE.AESEQ: AE.AESEQ -#> AE.AETERM: AE.AETERM -#> AE.AEMODIFY: AE.AEMODIFY -#> AE.AEDECOD: AE.AEDECOD -#> AE.AEBODSYS: AE.AEBODSYS -#> AE.AEBDSYCD: AE.AEBDSYCD -#> AE.AELLT: AE.AELLT -#> AE.AELLTCD: AE.AELLTCD -#> AE.AEPTCD: AE.AEPTCD -#> AE.AEHLT: AE.AEHLT -#> AE.AEHLTCD: AE.AEHLTCD -#> AE.AEHLGT: AE.AEHLGT -#> AE.AEHLGTCD: AE.AEHLGTCD -#> AE.AESOC: AE.AESOC -#> AE.AESOCCD: AE.AESOCCD -#> AE.AEDUR: AE.AEDUR -#> AE.AESEV: AE.AESEV -#> AE.AESEV or as per RAP: AE.AESEV or as per RAP -#> AE.AEACN: AE.AEACN -#> SUPPAE.QVAL where SUPPAE.QNAM="ACT1": SUPPAE.QVAL where SUPPAE.QNAM="ACT1" -#> SUPPAE.QVAL where QNAM="AETRTEM": SUPPAE.QVAL where QNAM="AETRTEM" -#> AE.AEREFID: AE.AEREFID -#> AE.AEACNOTH: AE.AEACNOTH -#> AE.AESER: AE.AESER -#> AE.AESCAN: AE.AESCAN -#> AE.AESCONG: AE.AESCONG -#> AE.AESDISAB: AE.AESDISAB -#> AE.AESDTH: AE.AESDTH -#> AE.AESHOSP: AE.AESHOSP -#> AE.AESLIFE: AE.AESLIFE -#> AE.AESOD: AE.AESOD -#> AE.AESMIE: AE.AESMIE -#> SUPPAE.QVAL where QNAM="AESPROT": SUPPAE.QVAL where QNAM="AESPROT" -#> AE.AEOUT: AE.AEOUT -#> AE.AEREL: AE.AEREL -#> AE.AETOXGR: AE.AETOXGR -#> Numeric version of AETOXGR: Numeric version of AETOXGR -#> SUPPAE.QVAL where SUPPAE.QNAM="GRADED": SUPPAE.QVAL where SUPPAE.QNAM="GRADED" -#> SUPPAE.QVAL where SUPPAE.QNAM="AEDLT": SUPPAE.QVAL where SUPPAE.QNAM="AEDLT" -#> SUPPAE.QVAL where SUPPAE.QNAM="AERDG1": SUPPAE.QVAL where SUPPAE.QNAM="AERDG1" -#> xx.STUDYID: xx.STUDYID -#> xx.USUBJID: xx.USUBJID -#> ADSL.SUBJID: ADSL.SUBJID -#> ADSL.AGEU: ADSL.AGEU -#> ADSL.SAFFL if needed: ADSL.SAFFL if needed -#> ADSL.FASFL if needed: ADSL.FASFL if needed -#> ADSL.ITTFL if needed: ADSL.ITTFL if needed -#> ADSL.ITTEFL if required: ADSL.ITTEFL if required -#> ADSL.PPROTFL if needed: ADSL.PPROTFL if needed -#> ADSL.TRTSDT: ADSL.TRTSDT -#> ADSL.TRTEDT: ADSL.TRTEDT -#> ADSL.TR01SDT: ADSL.TR01SDT -#> ADSL.TR01EDT: ADSL.TR01EDT -#> CE.CESEQ: CE.CESEQ -#> CE.CEREFID: CE.CEREFID -#> CE.CETERM: CE.CETERM -#> Study-specific definition: Study-specific definition -#> CE.CNDPREV: CE.CNDPREV -#> CE.CESTDTC: CE.CESTDTC -#> ADSL.DTHFL: ADSL.DTHFL -#> ADSL.DTHFN: ADSL.DTHFN -#> ADSL.DTHDT: ADSL.DTHDT -#> Cause of Death.: Cause of Death. -#> CM.STUDYID: CM.STUDYID -#> CM.USUBJID: CM.USUBJID -#> CM.SUBJID: CM.SUBJID -#> CM.CMSTDTC: CM.CMSTDTC -#> CM.CMSTRF: CM.CMSTRF -#> CM.CMENDTC: CM.CMENDTC -#> CM.CMENRF: CM.CMENRF -#> CM.CMSEQ: CM.CMSEQ -#> CM.CMREFID: CM.CMREFID -#> CM.CMTRT: CM.CMTRT -#> CM.CMCAT: CM.CMCAT -#> CM.CMSCAT: CM.CMSCAT -#> CM.CMINDC: CM.CMINDC -#> CM.CMDOSE: CM.CMDOSE -#> CM.CMDOSTXT: CM.CMDOSTXT -#> CM.CMDOSU: CM.CMDOSU -#> CM.CMDOSFRQ: CM.CMDOSFRQ -#> CM.CMROUTE: CM.CMROUTE -#> CM.CMPRESP: CM.CMPRESP -#> CM.CMCLAS: CM.CMCLAS -#> CM.CMCLASCD: CM.CMCLASCD -#> GSKDRUG.CMATC1 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C': GSKDRUG.CMATC1 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C' -#> GSKDRUG.CMATC2 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C': GSKDRUG.CMATC2 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C' -#> GSKDRUG.CMATC3 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C': GSKDRUG.CMATC3 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C' -#> GSKDRUG.CMATC4 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C': GSKDRUG.CMATC4 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C' -#> CM.CMDUR: CM.CMDUR -#> CM.CMOCCUR: CM.CMOCCUR -#> CM.CMDOSFRM: CM.CMDOSFRM -#> DA.STUDYID: DA.STUDYID -#> DA.USUBJID: DA.USUBJID -#> DA.SUBJID: DA.SUBJID -#> DA.VISITNUM: DA.VISITNUM -#> DA.VISIT: DA.VISIT -#> DA.DACAT: DA.DACAT -#> DA.DASCAT: DA.DASCAT -#> DA.DASEQ: DA.DASEQ -#> DA.DADTC: DA.DADTC -#> DA.DADY: DA.DADY -#> DA.DATEST and/or derived. Example contains "Compliance %": DA.DATEST and/or derived. Example contains "Compliance %" -#> DA.DATESTCD and/or derived: DA.DATESTCD and/or derived -#> ADSL.STUDYID: ADSL.STUDYID -#> ADSL.USUBJID: ADSL.USUBJID -#> FAAE.SUBJID: FAAE.SUBJID -#> FAAE.FATPTREF: FAAE.FATPTREF -#> FAAE.FATPTNUM: FAAE.FATPTNUM -#> FAAE.FATPT: FAAE.FATPT -#> DD.STUDYID: DD.STUDYID -#> DD.USUBJID: DD.USUBJID -#> ADSL.ACTARM: ADSL.ACTARM -#> ADSL.ENRLFL: ADSL.ENRLFL -#> ADSL.AP01SDT: ADSL.AP01SDT -#> ADSL.AP01SDTM: ADSL.AP01SDTM -#> ADSL.AP01EDT: ADSL.AP01EDT -#> ADSL.AP01EDTM: ADSL.AP01EDTM -#> DD.DDTPTREF: DD.DDTPTREF -#> DD.DDTPTNUM: DD.DDTPTNUM -#> DD.DDTPT: DD.DDTPT -#> DS.STUDYID: DS.STUDYID -#> DS.USUBJID: DS.USUBJID -#> DS.SUBJID: DS.SUBJID -#> DS.DSSTDTC: DS.DSSTDTC -#> DS.DSSEQ: DS.DSSEQ -#> DM.STUDYID: DM.STUDYID -#> DM.USUBJID: DM.USUBJID -#> DQ.SUBJID: DQ.SUBJID -#> SUPPDM.QVAL when QNAM=RACEOR or QNAM=RACEORx where x=1,2, ..., n.: SUPPDM.QVAL when QNAM=RACEOR or QNAM=RACEORx where x=1,2, ..., n. -#> ADSL.ARACE: ADSL.ARACE -#> ADSL.ARACEN: ADSL.ARACEN -#> ADSL.INVID: ADSL.INVID -#> ADSL.INVNAM: ADSL.INVNAM -#> ADSL.COUNTRY: ADSL.COUNTRY -#> ADSL.AGEGR1: ADSL.AGEGR1 -#> ADSL.AGEGR1N: ADSL.AGEGR1N -#> ADSL.RACEN: ADSL.RACEN -#> ADSL.ETHNIC: ADSL.ETHNIC -#> ADSL.ETHNICN: ADSL.ETHNICN -#> ADSL.TOTFL: ADSL.TOTFL -#> ADSL.TOTFN: ADSL.TOTFN -#> ADSL.ITTFN: ADSL.ITTFN -#> ADSL.PPROTFN: ADSL.PPROTFN -#> ADSL.COMPLFL: ADSL.COMPLFL -#> ADSL.COMPLFN: ADSL.COMPLFN -#> ADSL.RUNFFL: ADSL.RUNFFL -#> ADSL.RUNFFN: ADSL.RUNFFN -#> ADSL.SCRFFL: ADSL.SCRFFL -#> ADSL.SCRFFN: ADSL.SCRFFN -#> ADSL.ARM: ADSL.ARM -#> ADSL.ARMCD: ADSL.ARMCD -#> ADSL.TRTxxP, where xx is the value for APERIOD: ADSL.TRTxxP, where xx is the value for APERIOD -#> ADSL.TRTxxA, where xx is the value for APERIOD: ADSL.TRTxxA, where xx is the value for APERIOD -#> ADSL.RANDDT: ADSL.RANDDT -#> ADSL.RFSTDT: ADSL.RFSTDT -#> ADSL.RFENDT: ADSL.RFENDT -#> ADSL.APxxSDT, where xx is the value for APERIOD: ADSL.APxxSDT, where xx is the value for APERIOD -#> ADSL.APxxEDT, where xx is the value for APERIOD: ADSL.APxxEDT, where xx is the value for APERIOD +#> pred.AE.STUDYID: AE.STUDYID +#> pred.AE.USUBJID: AE.USUBJID +#> pred.AE.SUBJID: AE.SUBJID +#> pred.ADSL.SITEID: ADSL.SITEID +#> pred.ADSL.AGE: ADSL.AGE +#> pred.ADSL.SEX: ADSL.SEX +#> pred.ADSL.RACE: ADSL.RACE +#> pred.ADSL.ACOUNTRY: ADSL.ACOUNTRY +#> pred.ADSL.FASFL: ADSL.FASFL +#> pred.ADSL.ITTFL: ADSL.ITTFL +#> pred.ADSL.SAFFL: ADSL.SAFFL +#> pred.ADSL.PPROTFL: ADSL.PPROTFL +#> pred.ADSL.TRTxxPN that corresponds to the treatment selected in TRTP: ADSL.TRTxxPN that corresponds to the treatment selected in TRTP +#> pred.ADSL.TRTxxAN that corresponds to the treatment selected in TRTA: ADSL.TRTxxAN that corresponds to the treatment selected in TRTA +#> pred.ADSL.TRT01A: ADSL.TRT01A +#> pred.ADSL.TRT01AN: ADSL.TRT01AN +#> pred.ADSL.TRT01P: ADSL.TRT01P +#> pred.ADSL.TRT01PN: ADSL.TRT01PN +#> pred.ADSL.TRTSEQP: ADSL.TRTSEQP +#> pred.ADSL.TRTSEQPN: ADSL.TRTSEQPN +#> pred.ADSL.TRTSEQA: ADSL.TRTSEQA +#> pred.ADSL.TRTSEQAN: ADSL.TRTSEQAN +#> pred.AE.AESTDY: AE.AESTDY +#> pred.AE.AESTDTC: AE.AESTDTC +#> pred.AE.AEENDTC: AE.AEENDTC +#> pred.AE.AEENDY: AE.AEENDY +#> pred.AE.AESEQ: AE.AESEQ +#> pred.AE.AETERM: AE.AETERM +#> pred.AE.AEMODIFY: AE.AEMODIFY +#> pred.AE.AEDECOD: AE.AEDECOD +#> pred.AE.AEBODSYS: AE.AEBODSYS +#> pred.AE.AEBDSYCD: AE.AEBDSYCD +#> pred.AE.AELLT: AE.AELLT +#> pred.AE.AELLTCD: AE.AELLTCD +#> pred.AE.AEPTCD: AE.AEPTCD +#> pred.AE.AEHLT: AE.AEHLT +#> pred.AE.AEHLTCD: AE.AEHLTCD +#> pred.AE.AEHLGT: AE.AEHLGT +#> pred.AE.AEHLGTCD: AE.AEHLGTCD +#> pred.AE.AESOC: AE.AESOC +#> pred.AE.AESOCCD: AE.AESOCCD +#> pred.AE.AEDUR: AE.AEDUR +#> pred.AE.AESEV: AE.AESEV +#> pred.AE.AESEV or as per RAP: AE.AESEV or as per RAP +#> pred.AE.AEACN: AE.AEACN +#> pred.SUPPAE.QVAL where SUPPAE.QNAM="ACT1": SUPPAE.QVAL where SUPPAE.QNAM="ACT1" +#> pred.SUPPAE.QVAL where QNAM="AETRTEM": SUPPAE.QVAL where QNAM="AETRTEM" +#> pred.AE.AEREFID: AE.AEREFID +#> pred.AE.AEACNOTH: AE.AEACNOTH +#> pred.AE.AESER: AE.AESER +#> pred.AE.AESCAN: AE.AESCAN +#> pred.AE.AESCONG: AE.AESCONG +#> pred.AE.AESDISAB: AE.AESDISAB +#> pred.AE.AESDTH: AE.AESDTH +#> pred.AE.AESHOSP: AE.AESHOSP +#> pred.AE.AESLIFE: AE.AESLIFE +#> pred.AE.AESOD: AE.AESOD +#> pred.AE.AESMIE: AE.AESMIE +#> pred.SUPPAE.QVAL where QNAM="AESPROT": SUPPAE.QVAL where QNAM="AESPROT" +#> pred.AE.AEOUT: AE.AEOUT +#> pred.AE.AEREL: AE.AEREL +#> pred.AE.AETOXGR: AE.AETOXGR +#> pred.Numeric version of AETOXGR: Numeric version of AETOXGR +#> pred.SUPPAE.QVAL where SUPPAE.QNAM="GRADED": SUPPAE.QVAL where SUPPAE.QNAM="GRADED" +#> pred.SUPPAE.QVAL where SUPPAE.QNAM="AEDLT": SUPPAE.QVAL where SUPPAE.QNAM="AEDLT" +#> pred.SUPPAE.QVAL where SUPPAE.QNAM="AERDG1": SUPPAE.QVAL where SUPPAE.QNAM="AERDG1" +#> pred.xx.STUDYID: xx.STUDYID +#> pred.xx.USUBJID: xx.USUBJID +#> pred.ADSL.SUBJID: ADSL.SUBJID +#> pred.ADSL.AGEU: ADSL.AGEU +#> pred.ADSL.SAFFL if needed: ADSL.SAFFL if needed +#> pred.ADSL.FASFL if needed: ADSL.FASFL if needed +#> pred.ADSL.ITTFL if needed: ADSL.ITTFL if needed +#> pred.ADSL.ITTEFL if required: ADSL.ITTEFL if required +#> pred.ADSL.PPROTFL if needed: ADSL.PPROTFL if needed +#> pred.ADSL.TRTSDT: ADSL.TRTSDT +#> pred.ADSL.TRTEDT: ADSL.TRTEDT +#> pred.ADSL.TR01SDT: ADSL.TR01SDT +#> pred.ADSL.TR01EDT: ADSL.TR01EDT +#> pred.CE.CESEQ: CE.CESEQ +#> pred.CE.CEREFID: CE.CEREFID +#> pred.CE.CETERM: CE.CETERM +#> pred.Study-specific definition: Study-specific definition +#> pred.CE.CNDPREV: CE.CNDPREV +#> pred.CE.CESTDTC: CE.CESTDTC +#> pred.ADSL.DTHFL: ADSL.DTHFL +#> pred.ADSL.DTHFN: ADSL.DTHFN +#> pred.ADSL.DTHDT: ADSL.DTHDT +#> pred.Cause of Death.: Cause of Death. +#> pred.CM.STUDYID: CM.STUDYID +#> pred.CM.USUBJID: CM.USUBJID +#> pred.CM.SUBJID: CM.SUBJID +#> pred.CM.CMSTDTC: CM.CMSTDTC +#> pred.CM.CMSTRF: CM.CMSTRF +#> pred.CM.CMENDTC: CM.CMENDTC +#> pred.CM.CMENRF: CM.CMENRF +#> pred.CM.CMSEQ: CM.CMSEQ +#> pred.CM.CMREFID: CM.CMREFID +#> pred.CM.CMTRT: CM.CMTRT +#> pred.CM.CMCAT: CM.CMCAT +#> pred.CM.CMSCAT: CM.CMSCAT +#> pred.CM.CMINDC: CM.CMINDC +#> pred.CM.CMDOSE: CM.CMDOSE +#> pred.CM.CMDOSTXT: CM.CMDOSTXT +#> pred.CM.CMDOSU: CM.CMDOSU +#> pred.CM.CMDOSFRQ: CM.CMDOSFRQ +#> pred.CM.CMROUTE: CM.CMROUTE +#> pred.CM.CMPRESP: CM.CMPRESP +#> pred.CM.CMCLAS: CM.CMCLAS +#> pred.CM.CMCLASCD: CM.CMCLASCD +#> pred.GSKDRUG.CMATC1 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C': GSKDRUG.CMATC1 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C' +#> pred.GSKDRUG.CMATC2 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C': GSKDRUG.CMATC2 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C' +#> pred.GSKDRUG.CMATC3 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C': GSKDRUG.CMATC3 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C' +#> pred.GSKDRUG.CMATC4 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C': GSKDRUG.CMATC4 where GSKDRUG.CMDRGCOL = CM.DRGCOLCD and GSKDRUG.CMNC = 'C' +#> pred.CM.CMDUR: CM.CMDUR +#> pred.CM.CMOCCUR: CM.CMOCCUR +#> pred.CM.CMDOSFRM: CM.CMDOSFRM +#> pred.DA.STUDYID: DA.STUDYID +#> pred.DA.USUBJID: DA.USUBJID +#> pred.DA.SUBJID: DA.SUBJID +#> pred.DA.VISITNUM: DA.VISITNUM +#> pred.DA.VISIT: DA.VISIT +#> pred.DA.DACAT: DA.DACAT +#> pred.DA.DASCAT: DA.DASCAT +#> pred.DA.DASEQ: DA.DASEQ +#> pred.DA.DADTC: DA.DADTC +#> pred.DA.DADY: DA.DADY +#> pred.DA.DATEST and/or derived. Example contains "Compliance %": DA.DATEST and/or derived. Example contains "Compliance %" +#> pred.DA.DATESTCD and/or derived: DA.DATESTCD and/or derived +#> pred.ADSL.STUDYID: ADSL.STUDYID +#> pred.ADSL.USUBJID: ADSL.USUBJID +#> pred.FAAE.SUBJID: FAAE.SUBJID +#> pred.FAAE.FATPTREF: FAAE.FATPTREF +#> pred.FAAE.FATPTNUM: FAAE.FATPTNUM +#> pred.FAAE.FATPT: FAAE.FATPT +#> pred.DD.STUDYID: DD.STUDYID +#> pred.DD.USUBJID: DD.USUBJID +#> pred.ADSL.ACTARM: ADSL.ACTARM +#> pred.ADSL.ENRLFL: ADSL.ENRLFL +#> pred.ADSL.AP01SDT: ADSL.AP01SDT +#> pred.ADSL.AP01SDTM: ADSL.AP01SDTM +#> pred.ADSL.AP01EDT: ADSL.AP01EDT +#> pred.ADSL.AP01EDTM: ADSL.AP01EDTM +#> pred.DD.DDTPTREF: DD.DDTPTREF +#> pred.DD.DDTPTNUM: DD.DDTPTNUM +#> pred.DD.DDTPT: DD.DDTPT +#> pred.DS.STUDYID: DS.STUDYID +#> pred.DS.USUBJID: DS.USUBJID +#> pred.DS.SUBJID: DS.SUBJID +#> pred.DS.DSSTDTC: DS.DSSTDTC +#> pred.DS.DSSEQ: DS.DSSEQ +#> pred.DM.STUDYID: DM.STUDYID +#> pred.DM.USUBJID: DM.USUBJID +#> pred.DQ.SUBJID: DQ.SUBJID +#> pred.SUPPDM.QVAL when QNAM=RACEOR or QNAM=RACEORx where x=1,2, ..., n.: SUPPDM.QVAL when QNAM=RACEOR or QNAM=RACEORx where x=1,2, ..., n. +#> pred.ADSL.ARACE: ADSL.ARACE +#> pred.ADSL.ARACEN: ADSL.ARACEN +#> pred.ADSL.INVID: ADSL.INVID +#> pred.ADSL.INVNAM: ADSL.INVNAM +#> pred.ADSL.COUNTRY: ADSL.COUNTRY +#> pred.ADSL.AGEGR1: ADSL.AGEGR1 +#> pred.ADSL.AGEGR1N: ADSL.AGEGR1N +#> pred.ADSL.RACEN: ADSL.RACEN +#> pred.ADSL.ETHNIC: ADSL.ETHNIC +#> pred.ADSL.ETHNICN: ADSL.ETHNICN +#> pred.ADSL.TOTFL: ADSL.TOTFL +#> pred.ADSL.TOTFN: ADSL.TOTFN +#> pred.ADSL.ITTFN: ADSL.ITTFN +#> pred.ADSL.PPROTFN: ADSL.PPROTFN +#> pred.ADSL.COMPLFL: ADSL.COMPLFL +#> pred.ADSL.COMPLFN: ADSL.COMPLFN +#> pred.ADSL.RUNFFL: ADSL.RUNFFL +#> pred.ADSL.RUNFFN: ADSL.RUNFFN +#> pred.ADSL.SCRFFL: ADSL.SCRFFL +#> pred.ADSL.SCRFFN: ADSL.SCRFFN +#> pred.ADSL.ARM: ADSL.ARM +#> pred.ADSL.ARMCD: ADSL.ARMCD +#> pred.ADSL.TRTxxP, where xx is the value for APERIOD: ADSL.TRTxxP, where xx is the value for APERIOD +#> pred.ADSL.TRTxxA, where xx is the value for APERIOD: ADSL.TRTxxA, where xx is the value for APERIOD +#> pred.ADSL.RANDDT: ADSL.RANDDT +#> pred.ADSL.RFSTDT: ADSL.RFSTDT +#> pred.ADSL.RFENDT: ADSL.RFENDT +#> pred.ADSL.APxxSDT, where xx is the value for APERIOD: ADSL.APxxSDT, where xx is the value for APERIOD +#> pred.ADSL.APxxEDT, where xx is the value for APERIOD: ADSL.APxxEDT, where xx is the value for APERIOD #> Warning: The following variables have code ids not found in the codelist(s): #> ASTDT #> ASTTM @@ -798,12 +798,12 @@

Building Specification Readers

diff --git a/articles/Example.html b/articles/Example.html index 0e2939d..2ad244c 100644 --- a/articles/Example.html +++ b/articles/Example.html @@ -6,7 +6,7 @@ Example • metacore - + @@ -35,7 +35,7 @@ metacore - 0.1.2 + 0.1.3 @@ -173,7 +173,7 @@

Example

frame can be returned.

 subset_t
-#> # A tibble: 25 × 22
+#> # A tibble: 25 × 21
 #>    dataset variable key_seq order keep  core  supp_flag type     length label   
 #>    <chr>   <chr>      <int> <int> <lgl> <chr> <lgl>     <chr>     <int> <chr>   
 #>  1 DM      STUDYID        1     1 TRUE  NA    NA        text         12 Study I…
@@ -187,9 +187,9 @@ 
Example

 #>  9 DM      RFICDTC       NA     9 FALSE NA    NA        datetime     20 Date/Ti…
 #> 10 DM      RFPENDTC      NA    10 FALSE NA    NA        datetime     20 Date/Ti…
 #> # ℹ 15 more rows
-#> # ℹ 12 more variables: format <chr>, common <lgl>, code_id <chr>,
+#> # ℹ 11 more variables: format <chr>, common <lgl>, code_id <chr>,
 #> #   derivation_id <chr>, origin <chr>, where <chr>, sig_dig <int>,
-#> #   derivation <chr>, name <chr>, codes <list>, idvar <chr>, qeval <chr>
+#> # derivation <chr>, codes <list>, idvar <chr>, qeval <chr> @@ -73,11 +73,11 @@

All vignettes

diff --git a/authors.html b/authors.html index 33503bf..1526481 100644 --- a/authors.html +++ b/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • metacoreAuthors and Citation • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -57,7 +57,7 @@
-

Authors

+

Authors and Citation

@@ -77,6 +77,10 @@

Authors

Mike Stackhouse. Author.

+
  • +

    Tamara Senior. Author. +

    +

  • GSK/Atorus JPT. Copyright holder, funder.

    @@ -90,15 +94,16 @@

    Citation

    • -

    Fillmore C, Gans M, Tarasiewicz A, Stackhouse M (2023). +

    Fillmore C, Gans M, Tarasiewicz A, Stackhouse M, Senior T (2024). metacore: A Centralized Metadata Object Focus on Clinical Trial Data Programming Workflows. -https://atorus-research.github.io/metacore/, https://github.com/atorus-research/metacore. +R package version 0.1.3, https://github.com/atorus-research/metacore, https://atorus-research.github.io/metacore/. 

    @Manual{,
   title = {metacore: A Centralized Metadata Object Focus on Clinical Trial Data Programming Workflows},
-  author = {Christina Fillmore and Maya Gans and Ashley Tarasiewicz and Mike Stackhouse},
-  year = {2023},
-  note = {https://atorus-research.github.io/metacore/, https://github.com/atorus-research/metacore},
+  author = {Christina Fillmore and Maya Gans and Ashley Tarasiewicz and Mike Stackhouse and Tamara Senior},
+  year = {2024},
+  note = {R package version 0.1.3, https://github.com/atorus-research/metacore},
+  url = {https://atorus-research.github.io/metacore/},
 }
    @@ -108,11 +113,11 @@

    Citation

    diff --git a/index.html b/index.html index a384813..e134e9d 100644 --- a/index.html +++ b/index.html @@ -6,7 +6,7 @@ A Centralized Metadata Object Focus on Clinical Trial Data Programming Workflows • metacore - + @@ -35,7 +35,7 @@ metacore - 0.1.2 + 0.1.3 @@ -239,6 +239,7 @@

    Developers

  • Maya Gans
    Author
  • Ashley Tarasiewicz
    Author
  • Mike Stackhouse
    Author
    • +
  • Tamara Senior
    Author
  • GSK/Atorus JPT
    Copyright holder, funder
    • @@ -261,12 +262,12 @@

    Dev status

    diff --git a/news/index.html b/news/index.html index c483f56..9cc242b 100644 --- a/news/index.html +++ b/news/index.html @@ -1,5 +1,5 @@ -Changelog • metacoreChangelog • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -60,6 +60,17 @@

    Changelog

    Source: NEWS.md +
    +

    Metacore 0.1.3

    +
    +
    +

    Metacore 0.1.22023-03-02

    +

    Metacore 0.1.12022-12-07

    diff --git a/pkgdown.yml b/pkgdown.yml index 0ebef86..8eba479 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,8 +1,8 @@ -pandoc: 2.19.2 -pkgdown: 2.0.7 +pandoc: 3.1.11 +pkgdown: 2.0.9 pkgdown_sha: ~ articles: Building_Specification_Readers: Building_Specification_Readers.html Example: Example.html -last_built: 2023-07-24T08:02Z +last_built: 2024-05-01T14:34Z diff --git a/reference/MetaCore_filter.html b/reference/MetaCore_filter.html index 5669ca3..6f144c9 100644 --- a/reference/MetaCore_filter.html +++ b/reference/MetaCore_filter.html @@ -1,5 +1,5 @@ -Select method to subset by a single dataframe — MetaCore_filter • metacoreSelect method to subset by a single dataframe — MetaCore_filter • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -84,11 +84,11 @@

    Arguments

    diff --git a/reference/check_columns.html b/reference/check_columns.html index dbd42fb..f0a0c42 100644 --- a/reference/check_columns.html +++ b/reference/check_columns.html @@ -1,5 +1,5 @@ -Check all data frames include the correct types of columns — check_columns • metacoreCheck all data frames include the correct types of columns — check_columns • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -116,11 +116,11 @@

    Arguments

    diff --git a/reference/check_structure.html b/reference/check_structure.html index 40d66db..e6627d6 100644 --- a/reference/check_structure.html +++ b/reference/check_structure.html @@ -1,5 +1,5 @@ -Column Validation Function — check_structure • metacoreColumn Validation Function — check_structure • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -100,11 +100,11 @@

    Arguments

    diff --git a/reference/check_words.html b/reference/check_words.html index 41b4d61..1f08f4b 100644 --- a/reference/check_words.html +++ b/reference/check_words.html @@ -1,5 +1,5 @@ -Check Words in Column — check_words • metacoreCheck Words in Column — check_words • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -88,11 +88,11 @@

    Arguments

    diff --git a/reference/checks.html b/reference/checks.html index 18a245e..74ffc62 100644 --- a/reference/checks.html +++ b/reference/checks.html @@ -1,5 +1,5 @@ -Optional checks to consistency of metadata — check_inconsistent_labels • metacoreOptional checks to consistency of metadata — check_inconsistent_labels • metacoreCreate table — create_tbl • metacoreCreate table — create_tbl • metacoreDefine XML to DataDef Object — define_to_metacore • metacoreDefine XML to DataDef Object — define_to_metacore • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -94,11 +94,11 @@

    Value

    diff --git a/reference/get_control_term.html b/reference/get_control_term.html index 61eee9d..212806c 100644 --- a/reference/get_control_term.html +++ b/reference/get_control_term.html @@ -1,5 +1,5 @@ -Get Control Term — get_control_term • metacoreGet Control Term — get_control_term • metacoreGet Dataset Keys — get_keys • metacore + + +
    +
    + + + +
    +
    +
    +

    Get Dataset Keys

    + Source: R/metacore.R + +
    + +
    +

    Returns the dataset keys for a given dataset

    +
    + +
    + 
    get_keys(metacode, dataset)
    +
    + +
    +

    Arguments

    +
    metacode
    +

    metacore object

    + + +
    dataset
    +

    A dataset name

    + +
    +
    +

    Value

    + + +

    a 2-column tibble with dataset key variables and key sequence

    +
    + +
    +

    Examples

    + 
    if (FALSE) {
+meta_ex <- spec_to_metacore(metacore_example("p21_mock.xlsx"))
+get_keys(meta_ex, "AE")
+get_keys(meta_ex, AE)
+}
+
    +
    +
    + +
    + + +
    +

    Developed by Christina Fillmore, Maya Gans, Ashley Tarasiewicz, Mike Stackhouse, Tamara Senior, GSK/Atorus JPT.

    +
    + +
    +

    Site built with pkgdown 2.0.9.

    +
    + +
    + + + + + + + + diff --git a/reference/index.html b/reference/index.html index b36414d..70b169f 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,5 +1,5 @@ -Function reference • metacoreFunction reference • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -95,6 +95,10 @@

    All functions get_control_term()

    Get Control Term

    + +

    get_keys()

    + +

    Get Dataset Keys

    is_metacore()

    @@ -188,11 +192,11 @@

    All functions
    -

    Developed by Christina Fillmore, Maya Gans, Ashley Tarasiewicz, Mike Stackhouse, GSK/Atorus JPT.

    +

    Developed by Christina Fillmore, Maya Gans, Ashley Tarasiewicz, Mike Stackhouse, Tamara Senior, GSK/Atorus JPT.

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/reference/is_metacore.html b/reference/is_metacore.html index 6930628..fcb283d 100644 --- a/reference/is_metacore.html +++ b/reference/is_metacore.html @@ -1,5 +1,5 @@ -Is metacore object — is_metacore • metacoreIs metacore object — is_metacore • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -99,11 +99,11 @@

    Examples

    diff --git a/reference/load_metacore.html b/reference/load_metacore.html index 35ff089..0e9ef3f 100644 --- a/reference/load_metacore.html +++ b/reference/load_metacore.html @@ -1,5 +1,5 @@ -load metacore object — load_metacore • metacoreload metacore object — load_metacore • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -90,11 +90,11 @@

    Value

    diff --git a/reference/metacore.html b/reference/metacore.html index f8a6cc8..eca95ca 100644 --- a/reference/metacore.html +++ b/reference/metacore.html @@ -1,5 +1,5 @@ -R6 Class wrapper to create your own metacore object — metacore • metacoreR6 Class wrapper to create your own metacore object — metacore • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -122,11 +122,11 @@

    Arguments

    diff --git a/reference/metacore_example.html b/reference/metacore_example.html index e790b26..63065de 100644 --- a/reference/metacore_example.html +++ b/reference/metacore_example.html @@ -1,5 +1,5 @@ -Get path to metacore example — metacore_example • metacoreGet path to metacore example — metacore_example • metacorePipe operator — %>% • metacorePipe operator — %>% • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -78,11 +78,11 @@

    Pipe operator

    diff --git a/reference/read_all_sheets.html b/reference/read_all_sheets.html index 1d08411..a1b1642 100644 --- a/reference/read_all_sheets.html +++ b/reference/read_all_sheets.html @@ -1,5 +1,5 @@ -Read in all Sheets — read_all_sheets • metacoreRead in all Sheets — read_all_sheets • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -90,11 +90,11 @@

    Value

    diff --git a/reference/save_metacore.html b/reference/save_metacore.html index ddee07f..53653a7 100644 --- a/reference/save_metacore.html +++ b/reference/save_metacore.html @@ -1,5 +1,5 @@ -save metacore object — save_metacore • metacoresave metacore object — save_metacore • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -94,11 +94,11 @@

    Value

    diff --git a/reference/select_dataset.html b/reference/select_dataset.html index 4489cbb..7dbf8a0 100644 --- a/reference/select_dataset.html +++ b/reference/select_dataset.html @@ -1,5 +1,5 @@ -Select metacore object to single dataset — select_dataset • metacoreSelect metacore object to single dataset — select_dataset • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -98,11 +98,11 @@

    Value

    diff --git a/reference/spec_to_metacore.html b/reference/spec_to_metacore.html index f2ef715..ccf31f6 100644 --- a/reference/spec_to_metacore.html +++ b/reference/spec_to_metacore.html @@ -1,8 +1,8 @@ -Specification document to metacore object — spec_to_metacore • metacoreSpecification document to metacore object — spec_to_metacore • metacore @@ -20,7 +20,7 @@ metacore - 0.1.2 + 0.1.3 @@ -67,8 +67,8 @@

    Specification document to metacore object

    This function takes the location of an excel specification document and reads it in as a meta core object. At the moment it only supports specification in -the format of pinnacle 21 specifications. But, the @family spec builder can -be used as building blocks for bespoke specification documents

    +the format of pinnacle 21 specifications. But, the section level spec builder can +be used as building blocks for bespoke specification documents.

    @@ -106,11 +106,11 @@

    Value

    -

    Developed by Christina Fillmore, Maya Gans, Ashley Tarasiewicz, Mike Stackhouse, GSK/Atorus JPT.

    +

    Developed by Christina Fillmore, Maya Gans, Ashley Tarasiewicz, Mike Stackhouse, Tamara Senior, GSK/Atorus JPT.

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/reference/spec_type.html b/reference/spec_type.html index 0e0deb6..4cf5571 100644 --- a/reference/spec_type.html +++ b/reference/spec_type.html @@ -1,5 +1,5 @@ -Check the type of spec document — spec_type • metacoreCheck the type of spec document — spec_type • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -90,11 +90,11 @@

    Value

    diff --git a/reference/spec_type_to_codelist.html b/reference/spec_type_to_codelist.html index 0ca5c1e..81145dd 100644 --- a/reference/spec_type_to_codelist.html +++ b/reference/spec_type_to_codelist.html @@ -1,5 +1,5 @@ -Spec to codelist — spec_type_to_codelist • metacoreSpec to codelist — spec_type_to_codelist • metacoreSpec to derivation — spec_type_to_derivations • metacore metacore - 0.1.2 + 0.1.3 @@ -129,11 +129,11 @@

    See also

    diff --git a/reference/spec_type_to_ds_spec.html b/reference/spec_type_to_ds_spec.html index baf79f3..f3fe167 100644 --- a/reference/spec_type_to_ds_spec.html +++ b/reference/spec_type_to_ds_spec.html @@ -1,5 +1,5 @@ -Spec to ds_spec — spec_type_to_ds_spec • metacoreSpec to ds_spec — spec_type_to_ds_spec • metacoreSpec to ds_vars — spec_type_to_ds_vars • metacoreSpec to ds_vars — spec_type_to_ds_vars • metacoreSpec to value_spec — spec_type_to_value_spec • metacoreSpec to value_spec — spec_type_to_value_spec • metacoreSpec to var_spec — spec_type_to_var_spec • metacoreSpec to var_spec — spec_type_to_var_spec • metacoreXML to code list — xml_to_codelist • metacoreXML to code list — xml_to_codelist • metacoreXML to derivation table — xml_to_derivations • metacoreXML to derivation table — xml_to_derivations • metacoreXML to Data Set Spec — xml_to_ds_spec • metacoreXML to Data Set Spec — xml_to_ds_spec • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -99,11 +99,11 @@

    See also

    diff --git a/reference/xml_to_ds_vars.html b/reference/xml_to_ds_vars.html index 7f09203..6c9c272 100644 --- a/reference/xml_to_ds_vars.html +++ b/reference/xml_to_ds_vars.html @@ -1,5 +1,5 @@ -XML to Data Set Var table — xml_to_ds_vars • metacoreXML to Data Set Var table — xml_to_ds_vars • metacore @@ -17,7 +17,7 @@ metacore - 0.1.2 + 0.1.3 @@ -99,11 +99,11 @@

    See also

    diff --git a/reference/xml_to_value_spec.html b/reference/xml_to_value_spec.html index e426caa..6987635 100644 --- a/reference/xml_to_value_spec.html +++ b/reference/xml_to_value_spec.html @@ -1,5 +1,5 @@ -XML to value spec — xml_to_value_spec • metacoreXML to value spec — xml_to_value_spec • metacoreXML to variable spec — xml_to_var_spec • metacoreXML to variable spec — xml_to_var_spec • metacore