From 2ce0cd799c6300831937153f6df90e174308d5af Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 22 Oct 2024 14:13:34 +0200
Subject: [PATCH] Translated part of `UpdateRPlee11_cpp()` (#11)

---
 src/UpdateRPlee11_cpp.cpp | 89 ++++++++++++++++++++-------------------
 1 file changed, 45 insertions(+), 44 deletions(-)

diff --git a/src/UpdateRPlee11_cpp.cpp b/src/UpdateRPlee11_cpp.cpp
index e9b4d65..cc0ed0d 100644
--- a/src/UpdateRPlee11_cpp.cpp
+++ b/src/UpdateRPlee11_cpp.cpp
@@ -1,5 +1,5 @@
 #include <RcppArmadillo.h>
-#include "misc.h"
+#include "updateRP_genomic_cpp.h"
 // [[Rcpp::depends(RcppArmadillo)]]
 // [[Rcpp::export]]
 Rcpp::List UpdateRPlee11_cpp(
@@ -10,56 +10,57 @@ Rcpp::List UpdateRPlee11_cpp(
   const std::string method,
   const bool MRF_G
 ){
-  // p <- sobj$p
-  // tau <- hyperpar$tau
-  // cb <- hyperpar$cb
+  uint p = Rcpp::as<uint>(sobj["p"]);
+  double tau = Rcpp::as<double>(hyperpar["tau"]);
+  double cb = Rcpp::as<double>(hyperpar["cb"]);
 
-  // if (method == "Pooled" && MRF_G) {
-  //   x <- sobj$X
-  //   J <- hyperpar$J
-  //   ind.r <- hyperpar$ind.r
-  //   ind.d <- hyperpar$ind.d
-  //   ind.r_d <- hyperpar$ind.r_d
-  //   be.prop.sd.scale <- hyperpar$be.prop.sd.scale
-  //   be.ini <- ini$beta.ini
-  //   ga.ini <- ini$gamma.ini
-  //   h <- ini$h
+  arma::vec beta_ini;
+  arma::uvec acceptlee;
 
-  //   # erg = UpdateRP.lee11.helper(n, p, x, J, ind.r, ind.d, ind.r_d, be.ini, ga.ini, h, tau, cb)
-  //   erg <- updateRP_genomic_cpp(
-  //     p, x, J, ind.r, ind.d, ind.r_d,
-  //     be.ini, be.prop.sd.scale, ga.ini, h, tau, cb
-  //   )
+  if (method == "Pooled" && MRF_G) {
+    arma::mat x = Rcpp::as<arma::mat>(sobj["X"]);
+    uint J = Rcpp::as<uint>(hyperpar["J"]);
+    arma::mat ind_r = Rcpp::as<arma::mat>(hyperpar["ind.r"]);
+    arma::mat ind_d = Rcpp::as<arma::mat>(hyperpar["ind.d"]);
+    arma::mat ind_r_d = Rcpp::as<arma::mat>(hyperpar["ind.r_d"]);
+    double be_prop_sd_scale = Rcpp::as<double>(hyperpar["be.prop.sd.scale"]);
+    arma::vec be_ini = Rcpp::as<arma::vec>(ini["beta.ini"]);
+    arma::vec ga_ini = Rcpp::as<arma::vec>(ini["gamma.ini"]);
+    arma::vec h = Rcpp::as<arma::vec>(ini["h"]);
 
-  //   beta.ini <- as.vector(erg$be.ini)
-  //   acceptlee <- erg$acceptl
-  // } else {
-  //   beta.ini <- acceptlee <- vector("list", S)
-  //   for (g in 1:S) { # loop through subgroups
+    Rcpp::List erg = updateRP_genomic_cpp(
+      p, x, J, ind_r, ind_d, ind_r_d, be_ini, be_prop_sd_scale, ga_ini, h, tau,
+      cb
+    );
 
-  //     x <- sobj$X[[g]]
-  //     J <- hyperpar$J[[g]]
-  //     ind.r <- hyperpar$ind.r[[g]]
-  //     ind.d <- hyperpar$ind.d[[g]]
-  //     ind.r_d <- hyperpar$ind.r_d[[g]]
-  //     be.ini <- ini$beta.ini[[g]]
-  //     be.prop.sd.scale <- hyperpar$be.prop.sd.scale[[g]]
-  //     ga.ini <- ini$gamma.ini[[g]]
-  //     h <- ini$h[[g]]
+    beta_ini = Rcpp::as<arma::vec>(erg["be.ini"]);
+    acceptlee = Rcpp::as<arma::uvec>(erg["acceptl"]);
+  } else {
+    beta_ini = arma::zeros<arma::vec>(S);
+    acceptlee = arma::zeros<arma::uvec>(S);
+    for (uint g = 0; g < S; ++g) { // loop through subgroups
+      // x <- sobj$X[[g]]
+      // J <- hyperpar$J[[g]]
+      // ind.r <- hyperpar$ind.r[[g]]
+      // ind.d <- hyperpar$ind.d[[g]]
+      // ind.r_d <- hyperpar$ind.r_d[[g]]
+      // be.ini <- ini$beta.ini[[g]]
+      // be.prop.sd.scale <- hyperpar$be.prop.sd.scale[[g]]
+      // ga.ini <- ini$gamma.ini[[g]]
+      // h <- ini$h[[g]]
 
-  //     # erg = UpdateRP.lee11.helper(n, p, x, J, ind.r, ind.d, ind.r_d, be.ini, ga.ini, h, tau, cb)
-  //     erg <- updateRP_genomic_cpp(
-  //       p, x, J, ind.r, ind.d, ind.r_d,
-  //       be.ini, be.prop.sd.scale, ga.ini, h, tau, cb
-  //     )
+      // erg <- updateRP_genomic_cpp(
+      //   p, x, J, ind.r, ind.d, ind.r_d,
+      //   be.ini, be.prop.sd.scale, ga.ini, h, tau, cb
+      // )
 
-  //     beta.ini[[g]] <- as.vector(erg$be.ini)
-  //     acceptlee[[g]] <- erg$acceptl
-  //   }
-  // }
+      // beta.ini[[g]] <- as.vector(erg$be.ini)
+      // acceptlee[[g]] <- erg$acceptl
+    }
+  }
   Rcpp::List out = Rcpp::List::create(
-    Rcpp::Named("beta.ini") = NA_REAL, // TEMP
-    Rcpp::Named("acceptlee") = NA_REAL // TEMP
+    Rcpp::Named("beta.ini") = beta_ini,
+    Rcpp::Named("acceptlee") = acceptlee
   );
   return out;
 }