From 201ffe51622b88b2c118bc6df2cf8787c49d0c2f Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 22 Oct 2024 14:05:11 +0200
Subject: [PATCH] Added placeholder `UpdateRPlee11_cpp() (#11)

---
 R/RcppExports.R           |  4 ++++
 R/UpdateRPlee11.R         |  5 +++++
 src/RcppExports.cpp       | 16 ++++++++++++++++
 src/UpdateRPlee11_cpp.cpp | 18 ++++++++++++++++++
 src/init.c                |  2 ++
 5 files changed, 45 insertions(+)
 create mode 100644 src/UpdateRPlee11_cpp.cpp

diff --git a/R/RcppExports.R b/R/RcppExports.R
index 864264a..efb2372 100644
--- a/R/RcppExports.R
+++ b/R/RcppExports.R
@@ -5,6 +5,10 @@ UpdateGamma_cpp <- function(sobj, hyperpar, ini, S, method, MRF_G, MRF_2b) {
     .Call(`_BayesSurvive_UpdateGamma_cpp`, sobj, hyperpar, ini, S, method, MRF_G, MRF_2b)
 }
 
+UpdateRPlee11_cpp <- function(sobj, hyperpar, ini, S, method, MRF_G) {
+    .Call(`_BayesSurvive_UpdateRPlee11_cpp`, sobj, hyperpar, ini, S, method, MRF_G)
+}
+
 func_MCMC_graph_cpp <- function(sobj, hyperpar, ini, S, method, MRF_2b) {
     .Call(`_BayesSurvive_func_MCMC_graph_cpp`, sobj, hyperpar, ini, S, method, MRF_2b)
 }
diff --git a/R/UpdateRPlee11.R b/R/UpdateRPlee11.R
index dcb0aae..8a29f25 100755
--- a/R/UpdateRPlee11.R
+++ b/R/UpdateRPlee11.R
@@ -7,12 +7,17 @@
 #'
 #' @inheritParams BayesSurvive
 #' @inheritParams func_MCMC
+#' @inheritParams func_MCMC_graph
 #'
 #' @return A list object with component 'beta.ini' for the updated coefficients
 #' and component 'acceptlee' for the MCMC acceptance rate
 #'
 #' @export
 UpdateRPlee11 <- function(sobj, hyperpar, ini, S, method, MRF_G, cpp = FALSE) {
+  if (cpp) {
+    warning("Cpp not implemented. Rerouting to R implementation.")
+    return(UpdateRPlee11(sobj, hyperpar, ini, S, method, MRF_G))
+  }
   p <- sobj$p
   tau <- hyperpar$tau
   cb <- hyperpar$cb
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index b8513b1..f7659d4 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -28,6 +28,22 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// UpdateRPlee11_cpp
+Rcpp::List UpdateRPlee11_cpp(const Rcpp::List sobj, const Rcpp::List hyperpar, const Rcpp::List ini, const uint S, const std::string method, const bool MRF_G);
+RcppExport SEXP _BayesSurvive_UpdateRPlee11_cpp(SEXP sobjSEXP, SEXP hyperparSEXP, SEXP iniSEXP, SEXP SSEXP, SEXP methodSEXP, SEXP MRF_GSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::List >::type sobj(sobjSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::List >::type hyperpar(hyperparSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::List >::type ini(iniSEXP);
+    Rcpp::traits::input_parameter< const uint >::type S(SSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type method(methodSEXP);
+    Rcpp::traits::input_parameter< const bool >::type MRF_G(MRF_GSEXP);
+    rcpp_result_gen = Rcpp::wrap(UpdateRPlee11_cpp(sobj, hyperpar, ini, S, method, MRF_G));
+    return rcpp_result_gen;
+END_RCPP
+}
 // func_MCMC_graph_cpp
 Rcpp::List func_MCMC_graph_cpp(const Rcpp::List sobj, const Rcpp::List hyperpar, const Rcpp::List ini, const uint S, const std::string method, const bool MRF_2b);
 RcppExport SEXP _BayesSurvive_func_MCMC_graph_cpp(SEXP sobjSEXP, SEXP hyperparSEXP, SEXP iniSEXP, SEXP SSEXP, SEXP methodSEXP, SEXP MRF_2bSEXP) {
diff --git a/src/UpdateRPlee11_cpp.cpp b/src/UpdateRPlee11_cpp.cpp
new file mode 100644
index 0000000..dccb943
--- /dev/null
+++ b/src/UpdateRPlee11_cpp.cpp
@@ -0,0 +1,18 @@
+#include <RcppArmadillo.h>
+#include "misc.h"
+// [[Rcpp::depends(RcppArmadillo)]]
+// [[Rcpp::export]]
+Rcpp::List UpdateRPlee11_cpp(
+  const Rcpp::List sobj,
+  const Rcpp::List hyperpar,
+  const Rcpp::List ini,
+  const uint S,
+  const std::string method,
+  const bool MRF_G
+){
+  Rcpp::List out = Rcpp::List::create(
+    Rcpp::Named("beta.ini") = NA_REAL, // TEMP
+    Rcpp::Named("acceptlee") = NA_REAL // TEMP
+  );
+  return out;
+}
diff --git a/src/init.c b/src/init.c
index 678030f..0d9e72c 100644
--- a/src/init.c
+++ b/src/init.c
@@ -17,6 +17,7 @@ extern SEXP _BayesSurvive_updateRP_genomic_cpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEX
 extern SEXP _BayesSurvive_func_MCMC_graph_cpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
 extern SEXP _BayesSurvive_UpdateGamma_cpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
 extern SEXP _BayesSurvive_list_to_matrix(SEXP);
+extern SEXP _BayesSurvive_UpdateRPlee11_cpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
 
 static const R_CallMethodDef CallEntries[] = {
   {"_BayesSurvive_calJpost_helper_cpp",  (DL_FUNC) &_BayesSurvive_calJpost_helper_cpp,   9},
@@ -28,6 +29,7 @@ static const R_CallMethodDef CallEntries[] = {
   {"_BayesSurvive_func_MCMC_graph_cpp",  (DL_FUNC) &_BayesSurvive_func_MCMC_graph_cpp,   6},
   {"_BayesSurvive_UpdateGamma_cpp",      (DL_FUNC) &_BayesSurvive_UpdateGamma_cpp,       7},
   {"_BayesSurvive_list_to_matrix",       (DL_FUNC) &_BayesSurvive_list_to_matrix,        1},
+  {"_BayesSurvive_UpdateRPlee11_cpp",    (DL_FUNC) &_BayesSurvive_UpdateRPlee11_cpp,     6},
   {NULL, NULL, 0}
 };