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updated protocol files for additional subgroups #24

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30dab70
updated protocol files for additional subgroups
hc3292 May 7, 2025
5b9c628
added subgroup json files for protocol
hc3292 May 7, 2025
5bc5685
updated files for protocol
hc3292 May 7, 2025
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122 changes: 107 additions & 15 deletions Documents/Protocol/Appendix.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -59,16 +59,16 @@ removeMetforminAndInsulin <- function(json) {
}

# Age
youngerJson <- SqlRender::readSql(system.file("cohorts", "class", "ID101210000.json", package = "LegendT2dm"))
youngerCohort <- CirceR::cohortExpressionFromJson(removeMetforminAndInsulin(youngerJson))
youngerJson <- SqlRender::readSql(system.file("cohorts", "subgroups", "11759.json", package = "LegendT2dm"))
youngerCohort <- CirceR::cohortExpressionFromJson(youngerJson)
printInclusionCriteria(youngerCohort)

middleJson <- SqlRender::readSql(system.file("cohorts", "class", "ID101220000.json", package = "LegendT2dm"))
middleCohort <- CirceR::cohortExpressionFromJson(removeMetforminAndInsulin(middleJson))
middleJson <- SqlRender::readSql(system.file("cohorts", "subgroups", "11760.json", package = "LegendT2dm"))
middleCohort <- CirceR::cohortExpressionFromJson(middleJson)
printInclusionCriteria(middleCohort)

olderJson <- SqlRender::readSql(system.file("cohorts", "class", "ID101230000.json", package = "LegendT2dm"))
olderCohort <- CirceR::cohortExpressionFromJson(removeMetforminAndInsulin(olderJson))
olderJson <- SqlRender::readSql(system.file("cohorts", "subgroups", "11761.json", package = "LegendT2dm"))
olderCohort <- CirceR::cohortExpressionFromJson(olderJson)
printInclusionCriteria(olderCohort)
```

Expand Down Expand Up @@ -108,24 +108,116 @@ printCohortClose()
```

```{r heterogenity-cohort-renal, echo=FALSE, results="asis", warning=FALSE, message=FALSE}
# Renal
noRenalJson <- SqlRender::readSql(system.file("cohorts", "class", "ID101200001.json", package = "LegendT2dm"))
noRenalCohort <- CirceR::cohortExpressionFromJson(removeMetforminAndInsulin(noRenalJson))
# no Renal
no_renal_dz <- SqlRender::readSql(system.file("cohorts", "subgroups", "11734.json", package = "LegendT2dm"))
no_renalCohort <- CirceR::cohortExpressionFromJson(no_renal_dz)
printCohortEntryandInclusionCriteria(no_renalCohort, removeDescription = TRUE)

printInclusionCriteria(noRenalCohort)
# Renal no HD
renal_dz <- SqlRender::readSql(system.file("cohorts", "subgroups", "11732.json", package = "LegendT2dm"))
renalCohort <- CirceR::cohortExpressionFromJson(renal_dz)
printCohortEntryandInclusionCriteria(renalCohort, removeDescription = TRUE)

withRenalJson <- SqlRender::readSql(system.file("cohorts", "class", "ID101200002.json", package = "LegendT2dm"))
# Renal + HD
renal_hd = SqlRender::readSql(system.file("cohorts", "subgroups", "11733.json", package = "LegendT2dm"))
renalHDCohort <- CirceR::cohortExpressionFromJson(renal_hd)
printCohortEntryandInclusionCriteria(renalHDCohort, removeDescription = TRUE)

cohort <- RJSONIO::fromJSON(withRenalJson)
# concept sets in renal disease
printConceptSet(renalCohort$conceptSets[[1]])
printConceptSet(renalCohort$conceptSets[[2]])
printConceptSet(renalCohort$conceptSets[[3]])

withRenalCohort <- CirceR::cohortExpressionFromJson(removeMetforminAndInsulin(withRenalJson))
# dialysis
printConceptSet(renalCohort$conceptSets[[4]])

printInclusionCriteria(withRenalCohort)
printCohortClose()
```
```{r heterogenity-cohort-obesity, echo=FALSE, results="asis", warning=FALSE, message=FALSE}
# obesity
obesity <- SqlRender::readSql(system.file("cohorts", "subgroups", "11739.json", package = "LegendT2dm"))
obesityCohort <- CirceR::cohortExpressionFromJson(obesity)
printInclusionCriteria(obesityCohort, removeDescription = FALSE)

# concept sets
printConceptSet(obesityCohort$conceptSets[[2]])

printCohortClose()
```

```{r heterogenity-cohort-dm-severe, echo=FALSE, results="asis", warning=FALSE, message=FALSE}
# severe diabetes
dm_severe <- SqlRender::readSql(system.file("cohorts", "subgroups", "11746.json", package = "LegendT2dm"))
dm_severeCohort <- CirceR::cohortExpressionFromJson(dm_severe)
printInclusionCriteria(dm_severeCohort, removeDescription = FALSE)

# concept sets
printConceptSet(dm_severeCohort$conceptSets[[2]])

printCohortClose()
```

```{r heterogenity-cohort-dka, echo=FALSE, results="asis", warning=FALSE, message=FALSE}
# DKA
dka <- SqlRender::readSql(system.file("cohorts", "subgroups", "11741.json", package = "LegendT2dm"))
dkaCohort <- CirceR::cohortExpressionFromJson(dka)
printInclusionCriteria(dkaCohort, removeDescription = FALSE)

# concept sets
printConceptSet(dkaCohort$conceptSets[[1]])

printCohortClose()
```

```{r heterogenity-cohort-retinopathy, echo=FALSE, results="asis", warning=FALSE, message=FALSE}
# retinopathy
retin <- SqlRender::readSql(system.file("cohorts", "subgroups", "11743.json", package = "LegendT2dm"))
retinCohort <- CirceR::cohortExpressionFromJson(retin)
printInclusionCriteria(retinCohort, removeDescription = FALSE)

# concept sets
printConceptSet(retinCohort$conceptSets[[1]])

printConceptSet(withRenalCohort$conceptSets[[13]])
printCohortClose()
```

```{r heterogenity-cohort-HTN, echo=FALSE, results="asis", warning=FALSE, message=FALSE}
# essential HTN
htn <- SqlRender::readSql(system.file("cohorts", "subgroups", "11735.json", package = "LegendT2dm"))
htnCohort <- CirceR::cohortExpressionFromJson(htn)
printInclusionCriteria(htnCohort, removeDescription = FALSE)

# concept sets
printConceptSet(htnCohort$conceptSets[[1]])

printCohortClose()
```

```{r heterogenity-cohort-HLD, echo=FALSE, results="asis", warning=FALSE, message=FALSE}
# hyperlipedemia
hld <- SqlRender::readSql(system.file("cohorts", "subgroups", "11737.json", package = "LegendT2dm"))
hldCohort <- CirceR::cohortExpressionFromJson(hld)
printInclusionCriteria(hldCohort, removeDescription = FALSE)

# concept sets
printConceptSet(hldCohort$conceptSets[[1]])

printCohortClose()
```

```{r heterogenity-cohort-masld, echo=FALSE, results="asis", warning=FALSE, message=FALSE}
# MASLD
masld <- SqlRender::readSql(system.file("cohorts", "subgroups", "11710.json", package = "LegendT2dm"))
masldCohort <- CirceR::cohortExpressionFromJson(masld)
printInclusionCriteria(masldCohort, removeDescription = FALSE)

# concept sets
printConceptSet(masldCohort$conceptSets[[1]])

printCohortClose()
```


```{r drug-cohort, echo=FALSE, results="asis", warning=FALSE, message=FALSE}
drugCohortJson <- SqlRender::readSql(system.file("cohorts", "drug", "ID111100000.json", package = "LegendT2dm"))
drugCohort <- CirceR::cohortExpressionFromJson(drugCohortJson)
Expand Down
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