8000 Update disposition mapping with discontinuation rather than completion. by samussiah · Pull Request #746 · Gilead-BioStats/gsm · GitHub
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Update disposition mapping with discontinuation rather than completion. #746

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Merged
merged 2 commits into from
Sep 20, 2022
Merged

Update disposition mapping with discontinuation rather than completion. #746

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fa506f5
fix #692
samussiah Sep 20, 2022
dc6e065
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samussiah Sep 20, 2022
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4 changes: 2 additions & 2 deletions R/Disp_Map_Raw.R
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Expand Up @@ -81,9 +81,9 @@ Disp_Map_Raw <- function(
select(
SubjectID = lMapping[[strDomain]][["strIDCol"]],
DCReason = lMapping[[strDomain]][[glue::glue("str{strContext}DiscontinuationReasonCol")]],
Completion = lMapping[[strDomain]][[glue::glue("str{strContext}CompletionFlagCol")]]
Discontinuation = lMapping[[strDomain]][[glue::glue("str{strContext}DiscontinuationFlagCol")]]
) %>%
filter(!.data$Completion %in% lMapping[[strDomain]][[glue::glue("str{strContext}CompletionFlagVal")]]) %>%
filter(.data$Discontinuation %in% lMapping[[strDomain]][[glue::glue("str{strContext}DiscontinuationFlagVal")]]) %>%
mutate(Count = 1)

dfSUBJ_mapped <- dfs$dfSUBJ %>%
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8 changes: 4 additions & 4 deletions inst/mappings/mapping_rawplus.yaml
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10000
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Expand Up @@ -41,16 +41,16 @@ dfSTUDCOMP:
strIDCol: subjid
strStudyDiscontinuationReasonCol: compreas
strStudyDiscontinuationReasonVal: consent
strStudyCompletionFlagCol: compyn
strStudyCompletionFlagVal: "Y"
strStudyDiscontinuationFlagCol: compyn
strStudyDiscontinuationFlagVal: "N"
dfSDRGCOMP:
strIDCol: subjid
strTreatmentPhaseCol: datapagename # or foldername - temporary - should be phase
strTreatmentPhaseVal: Blinded Study Drug Completion
strTreatmentDiscontinuationReasonCol: sdrgreas
strTreatmentDiscontinuationReasonVal: withdrawal
strTreatmentCompletionFlagCol: sdrgyn
strTreatmentCompletionFlagVal: "Y"
strTreatmentDiscontinuationFlagCol: sdrgyn
strTreatmentDiscontinuationFlagVal: "N"
dfLB:
strIDCol: subjid
strVisitCol: visnam
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4 changes: 2 additions & 2 deletions inst/specs/Disp_Map_Raw_Study.yaml
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Expand Up @@ -2,10 +2,10 @@ dfSTUDCOMP:
vRequired:
- strIDCol
- strStudyDiscontinuationReasonCol
- strStudyCompletionFlagCol
- strStudyDiscontinuationFlagCol
vNACols:
- strStudyDiscontinuationReasonCol
- strStudyCompletionFlagCol
- strStudyDiscontinuationFlagCol
dfSUBJ:
vRequired:
- strIDCol
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4 changes: 2 additions & 2 deletions inst/specs/Disp_Map_Raw_Treatment.yaml
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Expand Up @@ -2,10 +2,10 @@ dfSDRGCOMP:
vRequired:
- strIDCol
- strTreatmentDiscontinuationReasonCol
- strTreatmentCompletionFlagCol
- strTreatmentDiscontinuationFlagCol
vNACols:
- strTreatmentDiscontinuationReasonCol
- strTreatmentCompletionFlagCol
- strTreatmentDiscontinuationFlagCol
dfSUBJ:
vRequired:
- strIDCol
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2 changes: 1 addition & 1 deletion man/md/Disp_Map_Raw_Study.md
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Expand Up @@ -6,4 +6,4 @@
|dfSUBJ |strIDCol |subjid |TRUE |FALSE |TRUE |
|dfSTUDCOMP |strIDCol |subjid |TRUE |FALSE |FALSE |
|dfSTUDCOMP |strStudyDiscontinuationReasonCol |compreas |TRUE |TRUE |FALSE |
|dfSTUDCOMP |strStudyCompletionFlagCol |compyn |TRUE |TRUE |FALSE |
|dfSTUDCOMP |strStudyDiscontinuationFlagCol |compyn |TRUE |TRUE |FALSE |
2 changes: 1 addition & 1 deletion man/md/Disp_Map_Raw_Treatment.md
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Expand Up @@ -6,4 +6,4 @@
|dfSUBJ |strIDCol |subjid |TRUE |FALSE |TRUE |
|dfSDRGCOMP |strIDCol |subjid |TRUE |FALSE |FALSE |
|dfSDRGCOMP |strTreatmentDiscontinuationReasonCol |sdrgreas |TRUE |TRUE |FALSE |
|dfSDRGCOMP |strTreatmentCompletionFlagCol |sdrgyn |TRUE |TRUE |FALSE |
|dfSDRGCOMP |strTreatmentDiscontinuationFlagCol |sdrgyn |TRUE |TRUE |FALSE |
10 changes: 5 additions & 5 deletions tests/testthat/_snaps/Disp_Map_Raw.md
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Expand Up @@ -23,12 +23,12 @@
{
"type": "character",
"attributes": {},
"value": ["strIDCol", "strStudyDiscontinuationReasonCol", "strStudyCompletionFlagCol"]
"value": ["strIDCol", "strStudyDiscontinuationReasonCol", "strStudyDiscontinuationFlagCol"]
},
{
"type": "character",
"attributes": {},
"value": ["strStudyDiscontinuationReasonCol", "strStudyCompletionFlagCol"]
"value": ["strStudyDiscontinuationReasonCol", "strStudyDiscontinuationFlagCol"]
}
]
},
Expand Down Expand Up @@ -75,7 +75,7 @@
"names": {
"type": "character",
"attributes": {},
"value": ["strIDCol", "strStudyDiscontinuationReasonCol", "strStudyDiscontinuationReasonVal", "strStudyCompletionFlagCol", "strStudyCompletionFlagVal"]
"value": ["strIDCol", "strStudyDiscontinuationReasonCol", "strStudyDiscontinuationReasonVal", "strStudyDiscontinuationFlagCol", "strStudyDiscontinuationFlagVal"]
}
},
"value": [
Expand All @@ -102,7 +102,7 @@
{
"type": "character",
"attributes": {},
"value": ["Y"]
"value": ["N"]
}
]
},
Expand Down Expand Up @@ -383,7 +383,7 @@

-- Checking Input Data for `Disp_Map_Raw_Study()` --

x "mapping" does not contain required parameters: strIDCol, strStudyDiscontinuationReasonCol, strStudyCompletionFlagCol
x "mapping" does not contain required parameters: strIDCol, strStudyDiscontinuationReasonCol, strStudyDiscontinuationFlagCol
x mapping is not a list()
x Non-character column names found in mapping:
x "mapping" does not contain required parameters: strIDCol, strSiteCol
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