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Add support for SCCS v6 #10

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Add support for SCCS v6 #10

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2a2f087
Modifications to support new SCCS v6 module specification structure
anthonysena Jun 9, 2025
fe6d9ca
Mandate SCCS v6 or higher
anthonysena Jun 9, 2025
84d09b8
backwards compatibility edits for SCCS
jreps Jun 16, 2025
fa3e428
Merge branch 'main' into sccs_v6
anthonysena Jun 19, 2025
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48 changes: 38 additions & 10 deletions inst/protocol/self-control-case-series.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,41 @@ output: html_document

package <- "SelfControlledCaseSeries"

# check using old or new SCCS setting
if('sccsAnalysesSpecifications' %in% names(SelfControlledCaseSeriesModuleSettings$settings)){

# check packageVersion >= 6.0.0 and warn if < 6.0.0
if(utils::compareVersion(
a = as.character(utils::packageVersion("SelfControlledCaseSeries")),
b = "6.0.0"
) == -1){
warning('Installed SelfControlledCaseSeries is less than version 6 but json created using package version 6 or higher.')
}

# set exposuresOutcomeList
sccsSettings <- SelfControlledCaseSeriesModuleSettings$settings$sccsAnalysesSpecifications

} else{

# check packageVersion < 6.0.0 and warn if >= 6.0.0
if(utils::compareVersion(
a = as.character(utils::packageVersion("SelfControlledCaseSeries")),
b = "6.0.0"
) == 0){
warning('Installed SelfControlledCaseSeries is version 6 or more but json created using package less than version 6.')
}

# set exposuresOutcomeList
sccsSettings <- SelfControlledCaseSeriesModuleSettings$settings

}

eo <- do.call(
what = rbind,
args = lapply(
X = 1:length(SelfControlledCaseSeriesModuleSettings$settings$exposuresOutcomeList),
X = 1:length(sccsSettings$exposuresOutcomeList),
FUN = function(k){
x <- SelfControlledCaseSeriesModuleSettings$settings$exposuresOutcomeList[[k]]
x <- sccsSettings$exposuresOutcomeList[[k]]
data.frame(
setting = ifelse(is.null(x$jsonId), 1, x$jsonId), #k,
outcomeId = rep(x$outcomeId, length(x$exposures)),
Expand All @@ -32,9 +61,9 @@ if(is.null(negativeControls)){
neg <- do.call(
what = rbind,
args = lapply(
X = 1:length(SelfControlledCaseSeriesModuleSettings$settings$exposuresOutcomeList),
X = 1:length(sccsSettings$exposuresOutcomeList),
FUN = function(k){
x <- SelfControlledCaseSeriesModuleSettings$settings$exposuresOutcomeList[[k]]
x <- sccsSettings$exposuresOutcomeList[[k]]
data.frame(
cohortId = rep(x$outcomeId, length(x$exposures)),
outcomeConceptId = rep(x$outcomeId, length(x$exposures)),
Expand Down Expand Up @@ -153,7 +182,7 @@ The design requires the user to specify the target population of interest, an op

In this specification there are ``r length(unique(eoOfInt$parentIdTarget))`` unique parent exposure cohorts (``r nrow(unique(eoOfInt[, c('exposureId', 'nestingId')]))`` unique exposure and indications combinations), see @sec-sccs-eo. There is a total of ``r length(unique(eoOfInt$nestingId))`` unique indications. A total of ``r length(unique(eoOfInt$parentIdOutcome))`` parent outcome cohorts (``r length(unique(eoOfInt$outcomeId))`` unique outcomes with subsets).

In total there are ``r length(SelfControlledCaseSeriesModuleSettings$settings$sccsAnalysisList)`` different self controlled case series analysis designs (see @sec-sccs-analysis).
In total there are ``r length(sccsSettings$sccsAnalysisList)`` different self controlled case series analysis designs (see @sec-sccs-analysis).


### Exposure Indication Outcomes {#sec-sccs-eo}
Expand Down Expand Up @@ -305,9 +334,9 @@ cat('\n\n')
```{r sccs_analyses, echo=FALSE, results = 'asis'}


for(i in 1:length(SelfControlledCaseSeriesModuleSettings$settings$sccsAnalysisList)){
for(i in 1:length(sccsSettings$sccsAnalysisList)){

analysisSetting <- SelfControlledCaseSeriesModuleSettings$settings$sccsAnalysisList[[i]]
analysisSetting <- sccsSettings$sccsAnalysisList[[i]]

cat(
paste0('#### Analysis ', analysisSetting$analysisId,': ', analysisSetting$description, ' \n'),
Expand Down Expand Up @@ -475,9 +504,8 @@ settingDf <- getSettingsTable(

```{r sccs_diagnostics, echo=FALSE, results = 'asis'}


if('sccsDiagnosticThresholds' %in% names(SelfControlledCaseSeriesModuleSettings$settings)){
diagSetting <- SelfControlledCaseSeriesModuleSettings$settings$sccsDiagnosticThresholds
if('sccsDiagnosticThresholds' %in% names(sccsSettings)){
diagSetting <- sccsSettings$sccsDiagnosticThresholds

diagSettings <- getSettingsTable(
package = package,
Expand Down