Fixing 'ORDER BY is ignored in subqueries without LIMIT' warning when…

… calling `createSccsIntervalData()`. Adding Eunomia unit test using splines

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SelfControlledCaseSeries
 Type: Package
 Title: Self-Controlled Case Series
-Version: 5.2.2
-Date: 2024-06-10
+Version: 5.2.3
+Date: 2024-06-20
 Authors@R: c(
   person("Martijn", "Schuemie", , "[email protected]", role = c("aut", "cre")),
 	person("Patrick", "Ryan", role = c("aut")),

NEWS.md

@@ -1,3 +1,11 @@
+SelfControlledCaseSeries 5.2.3
+==============================
+
+Bugfixes
+
+1. Fixing 'ORDER BY is ignored in subqueries without LIMIT' warning when calling `createSccsIntervalData()`.
+
+
 SelfControlledCaseSeries 5.2.2
 ==============================
 

R/SccsDataConversion.R

@@ -126,14 +126,12 @@ createSccsIntervalData <- function(studyPopulation,
   # Ensure all sorted bv caseId:
   cases <- studyPopulation$cases[order(studyPopulation$cases$caseId), ]
   outcomes <- studyPopulation$outcomes[order(studyPopulation$outcomes$caseId), ]
-  eras <- sccsData$eras %>%
-    arrange(.data$caseId)
   data <- Andromeda::andromeda()
 
   convertToSccs(
     cases = cases,
     outcomes = outcomes,
-    eras = eras,
+    eras = sccsData$eras,
     includeAge = !is.null(ageCovariateSettings),
     ageOffset = settings$ageOffset,
     ageDesignMatrix = settings$ageDesignMatrix,

src/AndromedaTableIterator.cpp

@@ -29,14 +29,13 @@ using namespace Rcpp;
 namespace ohdsi {
 namespace sccs {
 
-AndromedaTableIterator::AndromedaTableIterator(const List& _andromedaTable, const bool& _showProgressBar) :
+AndromedaTableIterator::AndromedaTableIterator(const List& _andromedaTable, const bool& _showProgressBar, const String& sortColumn) :
 progressBar(0),
 showProgressBar(_showProgressBar),
 completed(0),
 done(false) {
-
+  Environment dplyr = Environment::namespace_env("dplyr");
   if (showProgressBar){
-    Environment dplyr = Environment::namespace_env("dplyr");
     Function count = dplyr["count"];
     Function pull = dplyr["pull"];
     total = as<int>(pull(count(_andromedaTable)));
@@ -50,12 +49,13 @@ done(false) {
   }
   Environment dbplyr = Environment::namespace_env("dbplyr");
   Function remote_con = dbplyr["remote_con"];
+  Function arrange = dplyr["arrange"];
   Function sql_render = dbplyr["sql_render"];
   Environment dbi = Environment::namespace_env("DBI");
   Function dbSendQuery = dbi["dbSendQuery"];
 
   S4 connection = remote_con(_andromedaTable);
-  String sql = sql_render(_andromedaTable, connection);
+  String sql = sql_render(arrange(_andromedaTable), connection);
   resultSet = dbSendQuery(connection, sql);
 }
 

src/AndromedaTableIterator.h

@@ -31,7 +31,7 @@ namespace sccs {
 
 class AndromedaTableIterator {
 public:
-  AndromedaTableIterator(const List& _andromedaTable, const bool& _showProgressBar);
+  AndromedaTableIterator(const List& _andromedaTable, const bool& _showProgressBar, const String& sortColumn);
   ~AndromedaTableIterator();
   bool hasNext();
   List next();

src/PersonDataIterator.cpp

@@ -32,7 +32,7 @@ namespace sccs {
 
 
 PersonDataIterator::PersonDataIterator(const DataFrame& _cases, const DataFrame& _outcomes, const List& _eras) :
- erasIterator(_eras, true), casesObservationPeriodStartDate(0), casesCursor(0), outcomesCursor(0), erasCursor(0) {
+ erasIterator(_eras, true, "caseId"), casesObservationPeriodStartDate(0), casesCursor(0), outcomesCursor(0), erasCursor(0) {
 
   outcomesCaseId = _outcomes["caseId"];
   outcomesOutcomeDay = _outcomes["outcomeDay"];

tests/testthat/test-eunomia.R

@@ -69,10 +69,9 @@ test_that("Running multiple analyses against Eunomia", {
     endAnchor = "era start"
   )
 
-  # All outcomes occur at almost the same age, causing issues. Disable for now:
-  # ageSettings <- createAgeCovariateSettings(ageKnots = 5)
-  #
-  # seasonalitySettings <- createSeasonalityCovariateSettings(seasonKnots = 5)
+  calendarTimeSettings <- createCalendarTimeCovariateSettings(calendarTimeKnots = 5)
+
+  seasonalitySettings <- createSeasonalityCovariateSettings(seasonKnots = 5)
 
   covarPreExp <- createEraCovariateSettings(
     label = "Pre-exposure",
@@ -88,7 +87,9 @@ test_that("Running multiple analyses against Eunomia", {
       covarExposureOfInt,
       covarExposureOfInt2,
       covarPreExp
-    )
+    ),
+    calendarTimeCovariateSettings = calendarTimeSettings,
+    seasonalityCovariateSettings = seasonalitySettings
   )
 
   fitSccsModelArgs <- createFitSccsModelArgs()