get log-likelihood gradient R wrapper

NEWS.md

@@ -4,6 +4,7 @@ jni
 Changes:
 
 1. add JNI interface for manipulating Cyclops objects in an across-language persistent cache
+2. add `cyclopsGetLogLikelihoodGradient()`
 
 Cyclops v3.4.1
 ==============

R/ModelFit.R

@@ -339,6 +339,18 @@ fitCyclopsModel <- function(cyclopsData,
     return(fit)
 }
 
+#' @title Get full path to installed Cyclops library
+#'
+#' @description
+#' \code{cyclopsLibraryFileName} returns the full path to the installed Cyclops .so/.dll file
+#'
+#' @return String
+cyclopsLibraryFileName <- function() {
+    normalizePath(system.file("libs", .Platform$r_arch,
+                              paste0("Cyclops", .Platform$dynlib.ext),
+                              package = "Cyclops"))
+}
+
 #' @title Place Cyclops model fit object in a persistent cache
 #'
 #' @description

R/RcppExports.R

@@ -117,6 +117,10 @@
     .Call(`_Cyclops_cyclopsRunBootstrap`, inRcppCcdInterface, outFileName, treatmentId, replicates)
 }
 
+.cyclopsGetLogLikelihoodGradient <- function(inRcppCcdInterface) {
+    .Call(`_Cyclops_cyclopsGetLogLikelihoodGradient`, inRcppCcdInterface)
+}
+
 .cyclopsLogModel <- function(inRcppCcdInterface) {
     .Call(`_Cyclops_cyclopsLogModel`, inRcppCcdInterface)
 }

src/RcppCyclopsInterface.cpp

@@ -596,6 +596,28 @@ List cyclopsRunBootstrap(SEXP inRcppCcdInterface, const std::string& outFileName
     return list;
 }
 
+// [[Rcpp::export(".cyclopsGetLogLikelihoodGradient")]]
+NumericVector cyclopsGetLogLikelihoodGradient(SEXP inRcppCcdInterface) {
+    using namespace bsccs;
+
+    XPtr<RcppCcdInterface> interface(inRcppCcdInterface);
+
+    auto& ccd = interface->getCcd();
+    auto& data = interface->getModelData();
+
+
+    const auto offset = data.getHasOffsetCovariate();
+    const auto length = ccd.getBetaSize() - offset;
+
+    NumericVector gradient(length);
+
+    for (int i = 0; i < length; ++i) {
+        gradient[i] = ccd.getLogLikelihoodGradient(i + offset);
+    }
+
+    return gradient;
+}
+
 // [[Rcpp::export(".cyclopsLogModel")]]
 List cyclopsLogModel(SEXP inRcppCcdInterface) {
 	using namespace bsccs;

src/RcppExports.cpp

@@ -374,6 +374,17 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// cyclopsGetLogLikelihoodGradient
+NumericVector cyclopsGetLogLikelihoodGradient(SEXP inRcppCcdInterface);
+RcppExport SEXP _Cyclops_cyclopsGetLogLikelihoodGradient(SEXP inRcppCcdInterfaceSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< SEXP >::type inRcppCcdInterface(inRcppCcdInterfaceSEXP);
+    rcpp_result_gen = Rcpp::wrap(cyclopsGetLogLikelihoodGradient(inRcppCcdInterface));
+    return rcpp_result_gen;
+END_RCPP
+}
 // cyclopsLogModel
 List cyclopsLogModel(SEXP inRcppCcdInterface);
 RcppExport SEXP _Cyclops_cyclopsLogModel(SEXP inRcppCcdInterfaceSEXP) {
@@ -895,6 +906,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_Cyclops_cyclopsClearCacheForJava", (DL_FUNC) &_Cyclops_cyclopsClearCacheForJava, 0},
     {"_Cyclops_cyclopsFitModel", (DL_FUNC) &_Cyclops_cyclopsFitModel, 1},
     {"_Cyclops_cyclopsRunBootstrap", (DL_FUNC) &_Cyclops_cyclopsRunBootstrap, 4},
+    {"_Cyclops_cyclopsGetLogLikelihoodGradient", (DL_FUNC) &_Cyclops_cyclopsGetLogLikelihoodGradient, 1},
     {"_Cyclops_cyclopsLogModel", (DL_FUNC) &_Cyclops_cyclopsLogModel, 1},
     {"_Cyclops_cyclopsInitializeModel", (DL_FUNC) &_Cyclops_cyclopsInitializeModel, 4},
     {"_Cyclops_listGPUDevices", (DL_FUNC) &_Cyclops_listGPUDevices, 0},