Auto code formatting. Regenerating documentation.

OHDSI · May 25, 2022 · ce92cd4 · ce92cd4
1 parent 8e16cd9
commit ce92cd4
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Showing 95 changed files with 6,594 additions and 10,121 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: SelfControlledCaseSeries
 Type: Package
 Title: Self-Controlled Case Series
 Version: 3.3.0
-Date: 2022-04-04
+Date: 2022-05-25
 Authors@R: c(
   person("Martijn", "Schuemie", , "[email protected]", role = c("aut", "cre")),
 	person("Patrick", "Ryan", role = c("aut")),

diff --git a/R/Analyses.R b/R/Analyses.R
@@ -65,10 +65,12 @@ createSccsAnalysis <- function(analysisId = 1,
   checkmate::assertClass(createScriIntervalDataArgs, "args", null.ok = TRUE, add = errorMessages)
   checkmate::assertClass(fitSccsModelArgs, "args", add = errorMessages)
   checkmate::reportAssertions(collection = errorMessages)
-  if (toupper(design) == "SCCS" && is.null(createSccsIntervalDataArgs))
+  if (toupper(design) == "SCCS" && is.null(createSccsIntervalDataArgs)) {
     stop("Must provide createSccsIntervalDataArgs argument when design = 'SCCS'")
-  if (toupper(design) == "SCRI" && is.null(createScriIntervalDataArgs))
+  }
+  if (toupper(design) == "SCRI" && is.null(createScriIntervalDataArgs)) {
     stop("Must provide createScriIntervalDataArgs argument when design = 'SCRI'")
+  }
   analysis <- list()
   for (name in names(formals(createSccsAnalysis))) {
     analysis[[name]] <- get(name)
@@ -132,10 +134,12 @@ loadSccsAnalysisList <- function(file) {
 #' @export
 createExposureOutcome <- function(exposureId, outcomeId, ...) {
   errorMessages <- checkmate::makeAssertCollection()
-  if (!is.list(exposureId))
+  if (!is.list(exposureId)) {
     checkmate::assertInt(exposureId, add = errorMessages)
-  if (!is.list(outcomeId))
+  }
+  if (!is.list(outcomeId)) {
     checkmate::assertInt(outcomeId, add = errorMessages)
+  }
   checkmate::reportAssertions(collection = errorMessages)
 
   exposureOutcome <- list(...)

diff --git a/R/CovariateSettings.R b/R/CovariateSettings.R
@@ -87,8 +87,9 @@ createEraCovariateSettings <- function(includeEraIds = NULL,
   checkmate::assertLogical(allowRegularization, len = 1, add = errorMessages)
   checkmate::assertLogical(profileLikelihood, len = 1, add = errorMessages)
   checkmate::reportAssertions(collection = errorMessages)
-  if (allowRegularization && profileLikelihood)
+  if (allowRegularization && profileLikelihood) {
     stop("Cannot profile the likelihood of regularized covariates")
+  }
   if (!grepl("start$|end$", startAnchor, ignore.case = TRUE)) {
     stop("startAnchor should have value 'era start' or 'era end'")
   }
@@ -98,8 +99,9 @@ createEraCovariateSettings <- function(includeEraIds = NULL,
   isEnd <- function(anchor) {
     return(grepl("end$", anchor, ignore.case = TRUE))
   }
-  if (end < start && !isEnd(endAnchor))
+  if (end < start && !isEnd(endAnchor)) {
     stop("End day always precedes start day. Either pick a later end day, or set endAnchor to 'era end'.")
+  }
 
   # Make sure string is exact:
   if (isEnd(startAnchor)) {
@@ -315,8 +317,9 @@ createControlIntervalSettings <- function(includeEraIds = NULL,
   isEnd <- function(anchor) {
     return(grepl("end$", anchor, ignore.case = TRUE))
   }
-  if (end < start && !isEnd(endAnchor))
+  if (end < start && !isEnd(endAnchor)) {
     stop("End day always precedes start day. Either pick a later end day, or set endAnchor to 'era end'.")
+  }
 
   # Make sure string is exact:
   if (isEnd(startAnchor)) {
@@ -329,17 +332,19 @@ createControlIntervalSettings <- function(includeEraIds = NULL,
   } else {
     endAnchor <- "era start"
   }
-  analysis <- createEraCovariateSettings(includeEraIds = includeEraIds,
-                                         excludeEraIds = excludeEraIds,
-                                         label = "Control interval",
-                                         stratifyById = FALSE,
-                                         start = start,
-                                         startAnchor = startAnchor,
-                                         end = end,
-                                         endAnchor = endAnchor,
-                                         firstOccurrenceOnly = firstOccurrenceOnly,
-                                         splitPoints = c(),
-                                         allowRegularization = FALSE)
+  analysis <- createEraCovariateSettings(
+    includeEraIds = includeEraIds,
+    excludeEraIds = excludeEraIds,
+    label = "Control interval",
+    stratifyById = FALSE,
+    start = start,
+    startAnchor = startAnchor,
+    end = end,
+    endAnchor = endAnchor,
+    firstOccurrenceOnly = firstOccurrenceOnly,
+    splitPoints = c(),
+    allowRegularization = FALSE
+  )
   analysis$isControlInterval <- TRUE
   class(analysis) <- "ControlIntervalSettings"
   return(analysis)