fix type conversion in timeEffectMap

OHDSI · Nov 9, 2023 · a90dca2 · a90dca2
1 parent 18175ff
commit a90dca2
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Showing 9 changed files with 48 additions and 35 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -51,4 +51,4 @@ Suggests:
     microbenchmark,
     cmprsk,
     glmnet
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/R/DataManagement.R b/R/DataManagement.R
@@ -835,18 +835,29 @@ loadNewSqlCyclopsDataTimeEffectsDF <- function(object,
 #' @keywords internal
 loadNewSqlCyclopsDataTimeInteraction <- function(object,
                                                  covariateId,
-                                                 timeEffectMap) {
+                                                 timeEffectCovId,
+                                                 timeEffectTimeId) {
 
     if (!isInitialized(object)) stop("Object is no longer or improperly initialized.")
 
-    if (!all(timeEffectMap$covariateId %in% covariateId)) stop("Invalid covariateId for time effects.")
+    if (!all(timeEffectCovId %in% covariateId)) stop("Invalid covariateId for time effects.")
 
-    timeEffectMap$timeEffectId <- timeEffectMap$timeEffectId - 1 # Cpp start from 0
+    timeEffectTimeId <- timeEffectTimeId - 1 # Cpp start from 0
 
-    index <- .loadCyclopsDataTimeInteraction(object, timeEffectMap)
+    if (!bit64::is.integer64(timeEffectCovId)) {
+        timeEffectCovId <- bit64::as.integer64(timeEffectCovId)
+    }
+
+    if (!bit64::is.integer64(timeEffectTimeId)) {
+        timeEffectTimeId <- bit64::as.integer64(timeEffectTimeId)
+    }
+
+    index <- .loadCyclopsDataTimeInteraction(object,
+                                             timeEffectCovId,
+                                             timeEffectTimeId)
 
     if (!is.null(object$coefficientNames)) {
-        timeEffectName <- paste0("x", timeEffectMap$covariateId, ":time", timeEffectMap$timeEffectId + 1)
+        timeEffectName <- paste0("x", timeEffectCovId, ":time", timeEffectTimeId + 1)
         object$coefficientNames <- append(object$coefficientNames, timeEffectName)
     }
 }

diff --git a/R/NewDataConversion.R b/R/NewDataConversion.R
@@ -229,7 +229,8 @@ convertToCyclopsData.data.frame <- function(outcomes,
             if (!all(timeEffectMap$timeEffectId %in% 1:ncol(timeEffects))) stop("Invalid timeEffectId for interaction terms.")
             loadNewSqlCyclopsDataTimeInteraction(object = dataPtr,
                                                  covariateId = covariates$covariateId,
-                                                 timeEffectMap = timeEffectMap)
+                                                 timeEffectCovId = timeEffectMap$covariateId,
+                                                 timeEffectTimeId = timeEffectMap$timeEffectId)
         }
     }
 
@@ -392,7 +393,8 @@ convertToCyclopsData.tbl_dbi <- function(outcomes,
             if (!all(timeEffectMap$timeEffectId %in% 1:ncol(timeEffects))) stop("Invalid timeEffectId for interaction terms.")
             loadNewSqlCyclopsDataTimeInteraction(object = dataPtr,
                                                  covariateId = covariates$covariateId,
-                                                 timeEffectMap = timeEffectMap)
+                                                 timeEffectCovId = timeEffectMap$covariateId,
+                                                 timeEffectTimeId = timeEffectMap$timeEffectId)
         }
     }
 

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -282,8 +282,8 @@ getTimeVector <- function(object) {
     .Call(`_Cyclops_cyclopsLoadDataTimeEffectsDF`, x, timeEffects)
 }
 
-.loadCyclopsDataTimeInteraction <- function(x, timeEffectMap) {
-    .Call(`_Cyclops_cyclopsLoadDataTimeInteraction`, x, timeEffectMap)
+.loadCyclopsDataTimeInteraction <- function(x, covariateId, timeEffectId) {
+    .Call(`_Cyclops_cyclopsLoadDataTimeInteraction`, x, covariateId, timeEffectId)
 }
 
 .appendSqlCyclopsData <- function(x, oStratumId, oRowId, oY, oTime, cRowId, cCovariateId, cCovariateValue) {

diff --git a/man/convertToCyclopsData.Rd b/man/convertToCyclopsData.Rd
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -709,14 +709,15 @@ BEGIN_RCPP
 END_RCPP
 }
 // cyclopsLoadDataTimeInteraction
-int cyclopsLoadDataTimeInteraction(Environment x, DataFrame timeEffectMap);
-RcppExport SEXP _Cyclops_cyclopsLoadDataTimeInteraction(SEXP xSEXP, SEXP timeEffectMapSEXP) {
+int cyclopsLoadDataTimeInteraction(Environment x, const std::vector<double>& covariateId, const std::vector<double>& timeEffectId);
+RcppExport SEXP _Cyclops_cyclopsLoadDataTimeInteraction(SEXP xSEXP, SEXP covariateIdSEXP, SEXP timeEffectIdSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< Environment >::type x(xSEXP);
-    Rcpp::traits::input_parameter< DataFrame >::type timeEffectMap(timeEffectMapSEXP);
-    rcpp_result_gen = Rcpp::wrap(cyclopsLoadDataTimeInteraction(x, timeEffectMap));
+    Rcpp::traits::input_parameter< const std::vector<double>& >::type covariateId(covariateIdSEXP);
+    Rcpp::traits::input_parameter< const std::vector<double>& >::type timeEffectId(timeEffectIdSEXP);
+    rcpp_result_gen = Rcpp::wrap(cyclopsLoadDataTimeInteraction(x, covariateId, timeEffectId));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -840,7 +841,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_Cyclops_cyclopsLoadDataMultipleX", (DL_FUNC) &_Cyclops_cyclopsLoadDataMultipleX, 8},
     {"_Cyclops_cyclopsLoadDataX", (DL_FUNC) &_Cyclops_cyclopsLoadDataX, 7},
     {"_Cyclops_cyclopsLoadDataTimeEffectsDF", (DL_FUNC) &_Cyclops_cyclopsLoadDataTimeEffectsDF, 2},
-    {"_Cyclops_cyclopsLoadDataTimeInteraction", (DL_FUNC) &_Cyclops_cyclopsLoadDataTimeInteraction, 2},
+    {"_Cyclops_cyclopsLoadDataTimeInteraction", (DL_FUNC) &_Cyclops_cyclopsLoadDataTimeInteraction, 3},
     {"_Cyclops_cyclopsAppendSqlData", (DL_FUNC) &_Cyclops_cyclopsAppendSqlData, 8},
     {"_Cyclops_cyclopsGetInterceptLabel", (DL_FUNC) &_Cyclops_cyclopsGetInterceptLabel, 1},
     {"_Cyclops_cyclopsReadFileData", (DL_FUNC) &_Cyclops_cyclopsReadFileData, 2},

diff --git a/src/RcppModelData.cpp b/src/RcppModelData.cpp
@@ -640,19 +640,14 @@ int cyclopsLoadDataTimeEffectsDF(Environment x,
 
 // [[Rcpp::export(".loadCyclopsDataTimeInteraction")]]
 int cyclopsLoadDataTimeInteraction(Environment x,
-                                   DataFrame timeEffectMap) {
+                                   const std::vector<double>& covariateId,
+                                   const std::vector<double>& timeEffectId) {
 
     using namespace bsccs;
     XPtr<AbstractModelData> data = parseEnvironmentForPtr(x);
 
-    std::vector<std::pair<int, int>> tm;
-    NumericVector cId = timeEffectMap["covariateId"];
-    NumericVector tId = timeEffectMap["timeEffectId"];
-    for (int i = 0; i < timeEffectMap.nrows(); i++) {
-        tm.push_back(std::make_pair(cId[i], tId[i]));
-    }
-
-    return data->loadTimeInteraction(tm);
+    return data->loadTimeInteraction(reinterpret_cast<const std::vector<int64_t>&>(covariateId),
+		    reinterpret_cast<const std::vector<int64_t>&>(timeEffectId));
 }
 
 // NOTE:  IdType does not get exported into RcppExports, so hard-coded here

diff --git a/src/cyclops/ModelData.cpp b/src/cyclops/ModelData.cpp
@@ -399,21 +399,23 @@ int ModelData<RealType>::loadTimeEffectsDF(
 
 template <typename RealType>
 int ModelData<RealType>::loadTimeInteraction(
-        std::vector<std::pair<int, int>>& timeEffectMap) {
+        const std::vector<int64_t>& oCovariateId,
+        const std::vector<int64_t>& oTimeEffectId) {
 
     int numOfCov = getNumberOfColumns();
     int totalNumOfCov = numOfCov;
 
     // time effect with baseline covariates
-    for (auto t : timeEffectMap) {
+    for (size_t i = 0; i < oCovariateId.size(); i++) {
         // auto sharedPtrToColumnsVector = make_shared<IntVector>(column.getColumnsVector());
-        X.push_back(X.getColumn(t.first).getColumnsVectorPtr(),
-                    X.getColumn(t.first).getDataVectorPtr(),
-                    X.getFormatType(t.first));
+	int covId = getColumnIndexByName(oCovariateId[i]);
+        X.push_back(X.getColumn(covId).getColumnsVectorPtr(),
+                    X.getColumn(covId).getDataVectorPtr(),
+                    X.getFormatType(covId));
         X.getColumn(totalNumOfCov++).convertColumnToDense(getNumberOfRows());
         int index = getNumberOfColumns() - 1;
         X.getColumn(index).add_label(index);
-        mapTimeEffects.addTimeEffectColumn(t.second);
+        mapTimeEffects.addTimeEffectColumn(oTimeEffectId[i]);
     }
     mapTimeEffects.setNumInteraction(totalNumOfCov);
 

diff --git a/src/cyclops/ModelData.h b/src/cyclops/ModelData.h
@@ -232,7 +232,8 @@ class AbstractModelData {
     ) = 0;
 
     virtual int loadTimeInteraction(
-            std::vector<std::pair<int, int>>& timeEffectMap
+            const std::vector<int64_t>& covariateId,
+            const std::vector<int64_t>& timeEffectId
     ) = 0;
 
     virtual size_t append(
@@ -396,7 +397,8 @@ class ModelData : public AbstractModelData {
 	);
 
 	int loadTimeInteraction(
-	        std::vector<std::pair<int, int>>& timeEffectMap
+		const std::vector<int64_t>& covariateId,
+	        const std::vector<int64_t>& timeEffectId
 	);
 
 	const int* getPidVector() const;